4C5N

Structure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP and pyridoxal

Structural Biology Knowledgebase: 4C5N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4C5N

Classification: TRANSFERASE

Total Structure Weight: 122611.97

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOMETHYLPYRIMIDINE KINASE A, B, C, D 276 Staphylococcus aureus EC#: 2.7.1.35 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ACP
Query on ACP

A, B, C, D PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UEG
Query on UEG

D 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3- ol
C8 H11 N O3
LXNHXLLTXMVWPM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PXL
Query on PXL

A, B, C 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
PYRIDOXAL (Synonym)
C8 H9 N O3
RADKZDMFGJYCBB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.204
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.19 α = 90.00
b = 100.66 β = 90.00
c = 168.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-09-12
  • Released Date: 2014-03-19
  • Deposition author(s): Nodwell, M., Alte, F., Sieber, S.A., Schneider, S.

Revision History

  • 2014-04-16
    Type: Citation | Details: JRNL