3BGS

Structure of human purine nucleoside phosphorylase with L-DADMe-ImmH and phosphate

Structural Biology Knowledgebase: 3BGS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 3BGS

Classification: TRANSFERASE

Total Structure Weight: 32737.31

Macromolecule Entities
Molecule Chains Length Organism Details
purine nucleoside phosphorylase A 289 Homo sapiens EC#: 2.4.2.1 IUBMB
Mutation: G51S
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
DIH
Query on DIH

A 3-HYDROXY-4-HYDROXYMETHYL-1-(4-OXO-4,4A,5,7A- TETRAHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YLMETHYL)- PYRROLIDINIUM
(3R, (Synonym)
C12 H19 N4 O3
WFVGWLHAOKEIOJ-MFQSTILNSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DIH N/A in BindingDB
Ki: 0.38 nM  BindingMOAD
Ki: 0.38 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.218
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 142.80 α = 90.00
b = 142.80 β = 90.00
c = 167.35 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-27
  • Released Date: 2008-01-08
  • Deposition author(s): Murkin, A.S., Ramagopal, U.A., Almo, S.C., Schramm, V.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4