7AM2 | pdb_00007am2

Intermediate assembly of the Large subunit from Leishmania major mitochondrial ribosome

PDB DOI: https://doi.org/10.2210/pdb7AM2/pdb
NAKB: 7AM2
EM Map EMD-11821: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Leishmania tarentolae
Mutation(s): No

Deposited: 2020-10-07 Released: 2021-04-28
Deposition Author(s): Soufari, H., Waltz, F., Parrot, C., Bochler, A., Hashem, Y.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.

Soufari, H., Waltz, F., Parrot, C., Durrieu-Gaillard, S., Bochler, A., Kuhn, L., Sissler, M., Hashem, Y.

(2020) Proc Natl Acad Sci U S A 117: 29851-29861

PubMed: 33168716 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2011301117
Primary Citation Related Structures:
7AIH, 7AM2, 7ANE, 7AOR

PubMed Abstract:
Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.

Organizational Affiliation

Institut Européen de Chimie et Biologie, U1212 INSERM, UMR5320 CNRS, Université de Bordeaux, F-33600 Pessac, France.

Macromolecule Content

Total Structure Weight: 8,589.49 kDa
Atom Count: 139,523
Modeled Residue Count: 16,263
Deposited Residue Count: 41,533
Unique protein chains: 73
Unique nucleic acid chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L3-like protein	A	467	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
uL4m	B	436	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL_L9 domain-containing protein	C	262	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ribosomal protein L11	D [auth E]	346	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13-like protein	E [auth F]	171	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_L18e/L15P domain-containing protein	F [auth G]	374	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 50S ribosomal protein L17	G [auth I]	305	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
bL19m	H [auth J]	144	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
bL20m	I [auth K]	194	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
bL21m	J [auth L]	186	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
uL22m	K [auth M]	279	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
uL23m	L [auth N]	252	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
uL24m	M [auth O]	476	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
bL28m	N [auth Q]	234	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
uL29m	O [auth R]	480	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
uL30m	P [auth S]	409	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
bL32m	Q [auth T]	83	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
bL35m	R [auth V]	151	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
mL41	S [auth Z]	197	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
mL94	T [auth BA]	167	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
TRUD domain-containing protein	U [auth CA]	618	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
UA	V [auth UA]	203	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
mL95	W [auth BB]	156	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA uridylyltransferase	X [auth CB]	202	Leishmania tarentolae	Mutation(s): 0 EC: 2.7.7.52
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
mL67	Y [auth BK]	893	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
mL71	Z [auth BQ]	445	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
mL81	AA [auth BN]	344	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
mL98	BA [auth BE]	118	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ribosomal protein L14	CA [auth BO]	190	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
mL86	DA [auth At]	183	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
mL87	EA [auth Au]	186	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
mL53	FA [auth Ae]	311	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
mL63	GA [auth Af]	155	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
mL68	HA [auth Ah]	570	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
mL80	IA [auth Ap]	240	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
mL74	JA [auth Al]	346	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
L51_S25_CI-B8 domain-containing protein	KA [auth Ab]	262	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
mL42	LA [auth Aa]	195	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
mL52,mL52	MA [auth BP]	254	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
mL93	NA [auth Az]	152	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
mL75	OA [auth Am]	340	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
mL85	PA [auth As]	249	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
mL100	QA [auth BG]	1,347	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A504WW14 (Leishmania donovani) Explore A0A504WW14 Go to UniProtKB: A0A504WW14
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UniProt Group	A0A504WW14
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
mL49	RA [auth Ad]	237	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
mL89	SA [auth Aw]	187	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	TA [auth BH]	229	Leishmania tarentolae	Mutation(s): 0 EC: 5.2.1.8
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
mL72	UA [auth Aj]	503	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
mL84	VA [auth Ar]	205	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
mL76	WA [auth An]	331	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
mL99	XA [auth BF]	109	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
mL88	YA [auth Av]	192	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
mL70	ZA [auth BM]	457	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
mL59/64	AB [auth Ag]	244	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	BB [auth Bl]	266	Leishmania tarentolae	Mutation(s): 0 EC: 5.2.1.8
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM zinc-binding domain-containing protein	CB [auth Ax]	216	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
DNAj-like protein	DB [auth BS]	416	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
SpoU_methylase domain-containing protein	EB [auth BY], FB [auth BX]	569	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudouridylate synthase-like protein	GB [auth BZ]	413	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	HB [auth CC]	150	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
L0R8F8	IB [auth CD]	126	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
G domain-containing protein	JB [auth BT]	464	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase Der	KB [auth BU]	497	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
DEAD/DEAH box helicase-like protein	LB [auth BW]	776	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
G domain-containing protein	MB [auth BV]	787	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
mL78	NB [auth U7]	40	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
U6	OB [auth U6]	187	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
U1	PB [auth U1]	46	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
U3	QB [auth U3]	75	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
U4	RB [auth U4]	136	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
U5	SB [auth U5]	94	Leishmania tarentolae	Mutation(s): 0
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Reference Sequence

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Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
mL78	TB [auth BR]	301	Leishmania tarentolae	Mutation(s): 0
UniProt
Find proteins for A0A504XZ90 (Leishmania donovani) Explore A0A504XZ90 Go to UniProtKB: A0A504XZ90
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UniProt Group	A0A504XZ90
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Reference Sequence

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Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
U2	UB [auth U2]	37	Leishmania tarentolae	Mutation(s): 0
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Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
U8	ZB [auth U8]	59	Leishmania tarentolae	Mutation(s): 0
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Molecule	Chains	Length	Organism
Entity ID: 73
Ribosomal RNA	VB [auth 1]	19,000	Leishmania tarentolae
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Molecule	Chains	Length	Organism
Entity ID: 74
R1	WB [auth R1]	3	Leishmania tarentolae
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Molecule	Chains	Length	Organism
Entity ID: 75
R2	XB [auth R2]	35	Leishmania tarentolae
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Molecule	Chains	Length	Organism
Entity ID: 76
R5	YB [auth R5]	5	Leishmania tarentolae
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download:Ideal Coordinates CCD File SDF format, chain AC [auth BU] MOL2 format, chain AC [auth BU] mmCIF format, chain AC [auth BU]	AC [auth BU]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain AC [auth BU] Interactions & Density Focus chain AC [auth BU]
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain BC [auth BW] MOL2 format, chain BC [auth BW] mmCIF format, chain BC [auth BW]	BC [auth BW]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BC [auth BW] Interactions & Density Focus chain BC [auth BW]