1JNW

Active Site Structure of E. coli pyridoxine 5'-phosphate Oxidase

Structural Biology Knowledgebase: 1JNW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1JNW

Classification: OXIDOREDUCTASE

Total Structure Weight: 26618.37

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxine 5'-phosphate oxidase A 218 Escherichia coli EC#: 1.4.3.5 IUBMB
Mutation: M1M, M53M, M79M, M113M, M127M
Gene Name(s): pdxH b1638 JW1630
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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 L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.178
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 83.36 α = 90.00
b = 52.24 β = 101.45
c = 53.91 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-07-25
  • Released Date: 2001-08-01
  • Deposition author(s): di Salvo, M.L., Ko, T.P., Musayev, F.N., Raboni, S., Schirch, V., Safo, M.K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values