4EB8

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

Structural Biology Knowledgebase: 4EB8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 4EB8

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 109629.10

Macromolecule Entities
Molecule Chains Length Organism Details
Purine nucleoside phosphorylase A, B, C 324 Homo sapiens EC#: 2.4.2.1 IUBMB
Mutation: W16Y, G51S, W94Y, W178Y, H257W
Gene Name(s): PNP Gene View NP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
IM5
Query on IM5

A, B, C 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin- 1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin- 4-one
DADMe-ImmG (Synonym)
C12 H17 N5 O3
GSPTUGDLYPMLCQ-SFYZADRCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

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

B, C 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IM5 Ki: 7 nM (98) BindingDB

N/A in BindingMoad
Ki: 0.151 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.181
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 55.75 α = 90.00
b = 131.04 β = 90.00
c = 137.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-23
  • Released Date: 2013-02-06
  • Deposition author(s): Ho, M.C., Haapalainen, A.M., 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: --