5EFO

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.

PDB DOI: https://doi.org/10.2210/pdb5EFO/pdb

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

Deposited: 2015-10-24 Released: 2016-11-09
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: 1.63 Å
R-Value Free: 0.207
R-Value Work: 0.163
R-Value Observed: 0.165

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 uridine at 2.24 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 164.66 kDa
Atom Count: 13,396
Modelled Residue Count: 1,505
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, udp_1, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369... udp, udp_1, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTN Query on CTN Download Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	W [auth E], Z [auth F]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C₉ H₁₃ N₃ O₅ UHDGCWIWMRVCDJ-XVFCMESISA-N		Interactions Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain W [auth E] Focus chain Z [auth F]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CYT Query on CYT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	H [auth A] K [auth B] N [auth C] O [auth C] R [auth D] H [auth A], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	6-AMINOPYRIMIDIN-2(1H)-ONE C₄ H₅ N₃ O OPTASPLRGRRNAP-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E]	J [auth B], L [auth C], T [auth D], V [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth C] Focus chain T [auth D] Focus chain V [auth E] Interactions & Density Focus chain J [auth B] Focus chain L [auth C] Focus chain T [auth D] Focus chain V [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain X [auth F] SDF format, chain Y [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F]	Q [auth D], X [auth F], Y [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain Q [auth D] Focus chain X [auth F] Focus chain Y [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth C] SDF format, chain U [auth E] MOL2 format, chain G [auth A] MOL2 format, chain P [auth C] MOL2 format, chain U [auth E] mmCIF format, chain G [auth A] mmCIF format, chain P [auth C] mmCIF format, chain U [auth E]	G [auth A], P [auth C], U [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth C] Focus chain U [auth E] Interactions & Density Focus chain G [auth A] Focus chain P [auth C] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.207
R-Value Work: 0.163
R-Value Observed: 0.165
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.949	α = 67.54
b = 76.336	β = 73.74
c = 89.694	γ = 84.92

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description