9HMP | pdb_00009hmp

X-ray structure of S. cerevisiae threonylcarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP

PDB DOI: https://doi.org/10.2210/pdb9HMP/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-12-09 Released: 2025-12-24
Deposition Author(s): Hirschmann, J., Huber, E.M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free:
0.299 (Depositor), 0.290 (DCC)
R-Value Work:
0.255 (Depositor), 0.249 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural and biochemical characterization of yeast Tcd enzymes installing the epigenetic modification ct6A in tRNA

Hirschmann, J., Sonntag, R., Heiss, M., Wegrzyn, E., Heinemeyer, W., Carell, T., Huber, E.M.

To be published.

Macromolecule Content

Total Structure Weight: 175.95 kDa
Atom Count: 11,707
Modeled Residue Count: 1,451
Deposited Residue Count: 1,528
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA threonylcarbamoyladenosine dehydratase 1	A, B, C, D	382	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: TCD1, YHR003C EC: 6.1
UniProt
Find proteins for P38756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38756 Go to UniProtKB: P38756
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38756
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], P [auth C], T [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], Q [auth C], R [auth C], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] M [auth B] N [auth B] H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], S [auth C], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D]