1KY8

Crystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase

Structural Biology Knowledgebase: 1KY8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 1KY8

Classification: OXIDOREDUCTASE

Total Structure Weight: 54925.30

Macromolecule Entities
Molecule Chains Length Organism Details
glyceraldehyde-3-phosphate dehydrogenase A 501 Thermoproteus tenax EC#: 1.2.1.90 IUBMB
Gene Name(s): gapN
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NAP N/A in BindingDB
Kd: 1000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.208
  • Space Group: P 62 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 185.20 α = 90.00
b = 185.20 β = 90.00
c = 132.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-02-04
  • Released Date: 2003-02-04
  • Deposition author(s): Pohl, E., Brunner, N., Wilmanns, M., Hensel, R.

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