5C80

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution

PDB DOI: https://doi.org/10.2210/pdb5C80/pdb

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

Deposited: 2015-06-25 Released: 2016-07-20
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.
Funding Organization(s): RFBR

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.237
R-Value Work: 0.168
R-Value Observed: 0.172

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Balaev, V.V., Seregina, T.A., Mironov, A.S., Betzel, C., Mikhailov, A.M.

(2016) Crystallogr Rep 61: 954-973

DOI: https://doi.org/10.1134/S1063774516060134

Macromolecule Content

Total Structure Weight: 166.07 kDa
Atom Count: 12,408
Modelled Residue Count: 1,505
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URI Query on URI Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	AA [auth E] CA [auth F] G [auth A] L [auth B] R [auth C] AA [auth E], CA [auth F], G [auth A], L [auth B], R [auth C], V [auth D]	URIDINE C₉ H₁₂ N₂ O₆ DRTQHJPVMGBUCF-XVFCMESISA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	BA [auth E] DA [auth F] EA [auth F] FA [auth F] H [auth A] BA [auth E], DA [auth F], EA [auth F], FA [auth F], H [auth A], M [auth B], S [auth C], W [auth D], X [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C]	I [auth A], O [auth B], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth F] SDF format, chain N [auth B] SDF format, chain Y [auth D] MOL2 format, chain GA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain GA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain Y [auth D]	GA [auth F], N [auth B], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth F] Focus chain N [auth B] Focus chain Y [auth D] Interactions & Density Focus chain GA [auth F] Focus chain N [auth B] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain HA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain HA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	HA [auth F] J [auth A] K [auth A] P [auth B] U [auth C] HA [auth F], J [auth A], K [auth A], P [auth B], U [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain HA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain Q [auth B] MOL2 format, chain IA [auth F] MOL2 format, chain Q [auth B] mmCIF format, chain IA [auth F] mmCIF format, chain Q [auth B]	IA [auth F], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain IA [auth F] Focus chain Q [auth B] Interactions & Density Focus chain IA [auth F] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.237
R-Value Work: 0.168
R-Value Observed: 0.172
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.255	α = 71.81
b = 73.11	β = 77.19
c = 83.137	γ = 85.69

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-00952a

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2016-12-28
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description