2YXT

Human Pyridoxal Kinase

Structural Biology Knowledgebase: 2YXT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YXT

Classification: TRANSFERASE

Total Structure Weight: 72557.30

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxal kinase A, B 312 Homo sapiens EC#: 2.7.1.35 IUBMB
Gene Name(s): PDXK Gene View C21orf124 C21orf97 PKH PNK PRED79
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-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)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.206
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.63 α = 90.00
b = 115.29 β = 90.00
c = 172.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-04-27
  • Released Date: 2008-03-11
  • Deposition author(s): Safo, M.K., Musayev, F.N., Ko, T.P., Schirch, V.

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