5EPU | pdb_00005epu

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.

PDB DOI: https://doi.org/10.2210/pdb5EPU/pdb

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

Deposited: 2015-11-12 Released: 2016-11-23
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: 1.06 Å
R-Value Free:
0.122 (Depositor), 0.120 (DCC)
R-Value Work:
0.105 (Depositor), 0.110 (DCC)
R-Value Observed:
0.106 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.

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

To be published.

Macromolecule Content

Total Structure Weight: 164.61 kDa
Atom Count: 15,223
Modeled Residue Count: 1,509
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, udp_1, udp_2, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013160_01327, ERS013186_00327, ERS013199_00063... udp, udp_1, udp_2, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013160_01327, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377, ERS013212_00480 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
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain IA [auth F] Focus chain Q [auth B] Interactions & Density Focus chain IA [auth F] Focus chain Q [auth B]
CYT Query on CYT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth F] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	AA [auth E] G [auth A] GA [auth F] P [auth B] S [auth C] AA [auth E], G [auth A], GA [auth F], P [auth B], S [auth C], W [auth D]	6-AMINOPYRIMIDIN-2(1H)-ONE C₄ H₅ N₃ O OPTASPLRGRRNAP-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain G [auth A] Focus chain GA [auth F] Focus chain P [auth B] Focus chain S [auth C] Focus chain W [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	DA [auth F] H [auth A] I [auth A] M [auth B] V [auth D] DA [auth F], H [auth A], I [auth A], M [auth B], V [auth D], Y [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain DA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain V [auth D] Focus chain Y [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain HA [auth F] SDF format, chain T [auth C] MOL2 format, chain BA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain T [auth C] mmCIF format, chain BA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain T [auth C]	BA [auth E], HA [auth F], T [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain HA [auth F] Focus chain T [auth C] Interactions & Density Focus chain BA [auth E] Focus chain HA [auth F] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C]	N [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain N [auth B] Focus chain R [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain X [auth E] SDF format, chain Z [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth E]	EA [auth F] FA [auth F] J [auth A] K [auth A] O [auth B] EA [auth F], FA [auth F], J [auth A], K [auth A], O [auth B], X [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain FA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain X [auth E] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain FA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain X [auth E] Focus chain Z [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain L [auth A] SDF format, chain U [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain U [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain U [auth C]	CA [auth E], L [auth A], U [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain L [auth A] Focus chain U [auth C] Interactions & Density Focus chain CA [auth E] Focus chain L [auth A] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.06 Å
R-Value Free: 0.122 (Depositor), 0.120 (DCC)
R-Value Work: 0.105 (Depositor), 0.110 (DCC)
R-Value Observed: 0.106 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.848	α = 90
b = 96.715	β = 119.96
c = 92.89	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-11-23

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description