5LOK | pdb_00005lok

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution

PDB DOI: https://doi.org/10.2210/pdb5LOK/pdb

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

Deposited: 2016-08-09 Released: 2017-08-23
Deposition Author(s): Prokofev, I.I., Lashkov, A.A., Gabdoulkhakov, A.G., Dontsova, M.V., Betzel, C., Mikhailov, A.M.
Funding Organization(s): RFBR, Grant of President of Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.11 Å
R-Value Free:
0.136 (Depositor), 0.140 (DCC)
R-Value Work:
0.114 (Depositor), 0.120 (DCC)
R-Value Observed:
0.115 (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 of uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.11 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 166.06 kDa
Atom Count: 14,450
Modeled Residue Count: 1,509
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 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 FA [auth E] SDF format, chain I [auth A] SDF format, chain JA [auth F] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	FA [auth E] I [auth A] JA [auth F] P [auth B] U [auth C] FA [auth E], I [auth A], JA [auth F], P [auth B], U [auth C], Y [auth D]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C₉ H₁₃ N₃ O₅ UHDGCWIWMRVCDJ-XVFCMESISA-N		Interactions Focus chain FA [auth E] Focus chain I [auth A] Focus chain JA [auth F] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain FA [auth E] Focus chain I [auth A] Focus chain JA [auth F] Focus chain P [auth B] Focus chain U [auth C] Focus chain Y [auth D]
CYT Query on CYT Download Ideal Coordinates CCD File SDF format, chain GA [auth E] SDF format, chain J [auth A] SDF format, chain KA [auth F] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Z [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D]	GA [auth E] J [auth A] KA [auth F] Q [auth B] V [auth C] GA [auth E], J [auth A], KA [auth F], Q [auth B], V [auth C], X [auth D], Z [auth D]	6-AMINOPYRIMIDIN-2(1H)-ONE C₄ H₅ N₃ O OPTASPLRGRRNAP-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain J [auth A] Focus chain KA [auth F] Focus chain Q [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain GA [auth E] Focus chain J [auth A] Focus chain KA [auth F] Focus chain Q [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain LA [auth F] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C]	AA [auth D] HA [auth E] K [auth A] LA [auth F] R [auth B] AA [auth D], HA [auth E], K [auth A], LA [auth F], R [auth B], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain R [auth B] Focus chain W [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain DA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain DA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	DA [auth E], G [auth A], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain DA [auth E] Focus chain G [auth A] Focus chain O [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain H [auth A] SDF format, chain T [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain T [auth C] mmCIF format, chain EA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain T [auth C]	EA [auth E], H [auth A], T [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain H [auth A] Focus chain T [auth C] Interactions & Density Focus chain EA [auth E] Focus chain H [auth A] Focus chain T [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain IA [auth F] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C]	BA [auth E] CA [auth E] IA [auth F] M [auth B] N [auth B] BA [auth E], CA [auth E], IA [auth F], M [auth B], N [auth B], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain IA [auth F] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain IA [auth F] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.11 Å
R-Value Free: 0.136 (Depositor), 0.140 (DCC)
R-Value Work: 0.114 (Depositor), 0.120 (DCC)
R-Value Observed: 0.115 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.258	α = 69.35
b = 71.772	β = 72.17
c = 89.228	γ = 85.78

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-08-23

Deposition Author(s):

Funding Organization	Location	Grant Number
RFBR	Russian Federation	14-04-00952a
Grant of President of Russian Federation	Russian Federation	MK-9246.2016.3

Revision History (Full details and data files)

Version 1.0: 2017-08-23
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description