3PHB

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG

Ho, M.Cassera, M.B.Murkin, A.S.Almo, S.C.Schramm, V.L.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
E, Q, S, T, U, Y
324Homo sapiensMutation(s): 0 
Gene Names: PNP (NP)
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Go to Gene View: PNP
Go to UniProtKB:  P00491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
E, Q, S, T, U, Y
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
IM5
Query on IM5

Download SDF File 
Download CCD File 
E, Q, S, T, U, Y
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
C12 H17 N5 O3
GSPTUGDLYPMLCQ-SFYZADRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IM5Ki: 7 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 269.270α = 90.00
b = 52.632β = 90.33
c = 128.119γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2011-12-14
    Type: Non-polymer description
  • Version 1.2: 2017-11-08
    Type: Refinement description