5LHV

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 A resolution

PDB DOI: https://doi.org/10.2210/pdb5LHV/pdb

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

Deposited: 2016-07-13 Released: 2017-08-02
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Balaev, V.V., Betzel, C., Mikhailov, A.M.
Funding Organization(s): RFBR

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.178
R-Value Work: 0.145
R-Value Observed: 0.145

Starting Model: experimental
View more details

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 of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 165.26 kDa
Atom Count: 13,501
Modelled Residue Count: 1,503
Deposited Residue Count: 1,506
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	251	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
URI Query on URI Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain JA [auth E] SDF format, chain Q [auth B] SDF format, chain RA [auth F] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain W [auth C]	DA [auth D] I [auth A] JA [auth E] Q [auth B] RA [auth F] DA [auth D], I [auth A], JA [auth E], Q [auth B], RA [auth F], W [auth C]	URIDINE C₉ H₁₂ N₂ O₆ DRTQHJPVMGBUCF-XVFCMESISA-N		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain JA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain JA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain W [auth C]
URA Query on URA Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain J [auth A] SDF format, chain KA [auth E] SDF format, chain R [auth B] SDF format, chain SA [auth F] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain X [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain X [auth C]	EA [auth D] J [auth A] KA [auth E] R [auth B] SA [auth F] EA [auth D], J [auth A], KA [auth E], R [auth B], SA [auth F], X [auth C]	URACIL C₄ H₄ N₂ O₂ ISAKRJDGNUQOIC-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain J [auth A] Focus chain KA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A] Focus chain KA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain X [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain IA [auth E] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain QA [auth F] SDF format, chain V [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain V [auth C]	CA [auth D] G [auth A] H [auth A] IA [auth E] O [auth B] CA [auth D], G [auth A], H [auth A], IA [auth E], O [auth B], P [auth B], QA [auth F], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth F] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth F] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain HA [auth D] SDF format, chain N [auth A] SDF format, chain OA [auth E] SDF format, chain U [auth B] SDF format, chain VA [auth F] SDF format, chain WA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain WA [auth F]	BA [auth C] HA [auth D] N [auth A] OA [auth E] U [auth B] BA [auth C], HA [auth D], N [auth A], OA [auth E], U [auth B], VA [auth F], WA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain HA [auth D] Focus chain N [auth A] Focus chain OA [auth E] Focus chain U [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain HA [auth D] Focus chain N [auth A] Focus chain OA [auth E] Focus chain U [auth B] Focus chain VA [auth F] Focus chain WA [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain T [auth B] SDF format, chain UA [auth F] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain Z [auth C]	GA [auth D] L [auth A] MA [auth E] T [auth B] UA [auth F] GA [auth D], L [auth A], MA [auth E], T [auth B], UA [auth F], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth D] Focus chain L [auth A] Focus chain MA [auth E] Focus chain T [auth B] Focus chain UA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain L [auth A] Focus chain MA [auth E] Focus chain T [auth B] Focus chain UA [auth F] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain LA [auth E] SDF format, chain PA [auth E] SDF format, chain S [auth B] SDF format, chain TA [auth F] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain Y [auth C]	FA [auth D] K [auth A] LA [auth E] PA [auth E] S [auth B] FA [auth D], K [auth A], LA [auth E], PA [auth E], S [auth B], TA [auth F], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain K [auth A] Focus chain LA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain TA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain K [auth A] Focus chain LA [auth E] Focus chain PA [auth E] Focus chain S [auth B] Focus chain TA [auth F] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain M [auth A] SDF format, chain NA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth E]	AA [auth C], M [auth A], NA [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain M [auth A] Focus chain NA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain M [auth A] Focus chain NA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.178
R-Value Work: 0.145
R-Value Observed: 0.145
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.223	α = 69.7
b = 71.648	β = 72.7
c = 88.878	γ = 86.24

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
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: 2017-08-02

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description