5MIW

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

Starting Model: experimental
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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 uracil at 1.28 A.

Prokofev, I.I.Lashkov, A.A.Balaev, V.V.Gabdoulkhakov, A.G.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_1
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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
URA
Query on URA

Download Ideal Coordinates CCD File 
DA [auth D]
IA [auth E]
J [auth A]
LA [auth F]
O [auth B]
DA [auth D],
IA [auth E],
J [auth A],
LA [auth F],
O [auth B],
W [auth C]
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
SO4
Query on SO4

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K [auth A],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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EA [auth D]
FA [auth D]
JA [auth E]
L [auth A]
MA [auth F]
EA [auth D],
FA [auth D],
JA [auth E],
L [auth A],
MA [auth F],
NA [auth F],
Q [auth B],
R [auth B],
X [auth C],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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N [auth B],
V [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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AA [auth D]
BA [auth D]
G [auth A]
GA [auth E]
KA [auth F]
AA [auth D],
BA [auth D],
G [auth A],
GA [auth E],
KA [auth F],
M [auth B],
T [auth C],
U [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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CA [auth D]
H [auth A]
HA [auth E]
I [auth A]
S [auth B]
CA [auth D],
H [auth A],
HA [auth E],
I [auth A],
S [auth B],
Z [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.513α = 69.22
b = 71.948β = 72.2
c = 89.332γ = 85.6
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description