3MBH

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.167

Literature

Macromolecules
Sequence Display for 3MBH

Classification: TRANSFERASE

Total Structure Weight: 201740.16

Macromolecule Entities
Molecule Chains Length Organism Details
Putative phosphomethylpyrimidine kinase A, B, C..., D, E, FA, B, C, D, E, F 291 Bacteroides thetaiotaomicron EC#: 2.7.1.35 IUBMB
Gene Name(s): BT_4458
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PXL
Query on PXL

A, B, C, D, E, F 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
PYRIDOXAL (Synonym)
C8 H9 N O3
RADKZDMFGJYCBB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C, E, F CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D, E, F L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 93.72 α = 90.00
b = 138.37 β = 90.00
c = 143.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-25
  • Released Date: 2010-06-02
  • Deposition author(s): Joint Center for Structural Genomics (JCSG)

Revision History

  • 2011-07-13
    Type: Advisory, Version format compliance