5LOK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 

Starting Model: experimental
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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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine phosphorylase
A, B, C, D, E
A, B, C, D, E, F
253Vibrio choleraeMutation(s): 0 
Gene Names: udpudp_1DN30_1909
EC: 2.4.2.3
UniProt
Find proteins for Q9K4U1 (Vibrio cholerae)
Explore Q9K4U1 
Go to UniProtKB:  Q9K4U1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K4U1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CTN
Query on CTN

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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
CYT
Query on CYT

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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
SO4
Query on SO4

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L [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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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
EDO
Query on EDO

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DA [auth E],
G [auth A],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

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EA [auth E],
H [auth A],
T [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.11 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.258α = 69.35
b = 71.772β = 72.17
c = 89.228γ = 85.78
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RFBRRussian Federation14-04-00952a
Grant of President of Russian FederationRussian FederationMK-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