4KGD

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate

Structural Biology Knowledgebase: 4KGD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.150
  • R-Value Work: 0.127

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KGD

Classification: OXIDOREDUCTASE

Total Structure Weight: 135941.22

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate oxidase A, B 603 Lactobacillus plantarum EC#: 1.2.3.3 IUBMB
Gene Name(s): pox5 JDM1_2870

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

A, B FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TDP
Query on TDP

A, B THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.150
  • R-Value Work: 0.127
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 119.28 α = 90.00
b = 154.16 β = 90.00
c = 165.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-29
  • Released Date: 2013-06-12
  • Deposition author(s): Neumann, P., Tittmann, K.

Revision History

  • 2013-08-07
    Type: Citation | Details: Citation update
  • 2013-06-26
    Type: Citation | Details: Citation update