4U2K | pdb_00004u2k

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with anticancer compound at 2.13 A resolution

PDB DOI: https://doi.org/10.2210/pdb4U2K/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-17 Released: 2015-07-29
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with new anticancer compound at 1.17 A resolution

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 164.31 kDa
Atom Count: 11,998
Modelled Residue Count: 1,480
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine phosphorylase	A, B, C, D, E A, B, C, D, E, F	253	Vibrio cholerae	Mutation(s): 0 Gene Names: udp, DN30_1909, VC39_02535, VC78_02550, VS27_10630, WG08_05660 EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae) Explore Q9K4U1 Go to UniProtKB: Q9K4U1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9K4U1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M5F Query on M5F Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain U [auth F] MOL2 format, chain O [auth D] MOL2 format, chain U [auth F] mmCIF format, chain O [auth D] mmCIF format, chain U [auth F]	O [auth D], U [auth F]	1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione C₇ H₁₁ F N₄ O₂ ZBKWVMMCABYTAU-BYPYZUCNSA-N		Interactions Focus chain O [auth D] Focus chain U [auth F] Interactions & Density Focus chain O [auth D] Focus chain U [auth F]
4WR Query on 4WR Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D]	J [auth B], P [auth D]	1-[(2R)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione C₇ H₁₁ F N₄ O₂ ZBKWVMMCABYTAU-SCSAIBSYSA-N		Interactions Focus chain J [auth B] Focus chain P [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain T [auth F] MOL2 format, chain T [auth F] mmCIF format, chain T [auth F]	T [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain T [auth F] Interactions & Density Focus chain T [auth F]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain Q [auth E] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth E] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth E]	M [auth D], Q [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain Q [auth E] Interactions & Density Focus chain M [auth D] Focus chain Q [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain R [auth E] SDF format, chain S [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E]	G [auth A] H [auth A] I [auth B] K [auth C] L [auth C] G [auth A], H [auth A], I [auth B], K [auth C], L [auth C], R [auth E], S [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain R [auth E] Focus chain S [auth E]