1YBD

Crystal structure analysis of uridylate kinase from Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure analysis of uridylate kinase from Neisseria meningitidis

Kumaran, D.Swaminathan, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uridylate kinaseA, B, C239Neisseria meningitidisMutation(s): 12 
Gene Names: pyrH
EC: 2.7.4 (PDB Primary Data), 2.7.4.22 (UniProt)
Find proteins for P65932 (Neisseria meningitidis serogroup B (strain MC58))
Explore P65932 
Go to UniProtKB:  P65932
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.292α = 90
b = 158.292β = 90
c = 58.741γ = 120
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data scaling
SHELXDphasing
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance