4GKA

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with phosphate

Structural Biology Knowledgebase: 4GKA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 4GKA

Classification: transferase

Total Structure Weight: 217518.34

Macromolecule Entities
Molecule Chains Length Organism Details
Purine nucleoside phosphorylase A, B, C..., D, E, FA, B, C, D, E, F 324 Homo sapiens EC#: 2.4.2.1 IUBMB
Fragment: NONE
Mutation: W16Y, G51S, W94Y, W178Y, H257W
Gene Name(s): PNP Gene View NP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

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

C, F GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.188
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.88 α = 90.00
b = 233.67 β = 97.33
c = 70.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-10
  • Released Date: 2013-02-06
  • Deposition author(s): Haapalainen, A.M., Ho, M.C., Suarez, J.J., Almo, S.C., Schramm, V.L.

Revision History

  • 2013-03-13
    Type: Citation | Details: Citation update
  • 2013-03-06
    Type: Citation | Details: --