4EAR

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

Structural Biology Knowledgebase: 4EAR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4EAR

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 109558.95

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, H257X
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
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IM5 Ki: 7 nM (98) BindingDB

N/A in BindingMoad
Kd: 0.151 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
FT6
Query on FT6
A, B, C L-PEPTIDE LINKING C11 H11 F N2 O2 TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.175
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 55.92 α = 90.00
b = 131.10 β = 90.00
c = 137.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-22
  • 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: --