3K8O

Crystal structure of human purine nucleoside phosphorylase in complex with DATMe-ImmH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 

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 DATMe-Immucillin H

Ho, M.Rinaldo-matthis, A.Almo, S.C.Schramm, V.L.

(2010) Proc.Natl.Acad.Sci.USA --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
E, Q, S, T, U, Y
289Homo sapiensMutation(s): 1 
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
SO4
Query on SO4

Download SDF File 
Download CCD File 
E, Q, S, T, U, Y
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
229
Query on 229

Download SDF File 
Download CCD File 
E, Q, S, T, U, Y
7-({[(1R,2S)-2,3-DIHYDROXY-1-(HYDROXYMETHYL)PROPYL]AMINO}METHYL)-3,5-DIHYDRO-4H-PYRROLO[3,2-D]PYRIMIDIN-4-ONE
C11 H16 N4 O4
CGYSFECPLYEOMH-HTQZYQBOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
229Kd: 0 nM (99) BINDINGDB
229Ki: 8.6 - 780 nM (99) BINDINGDB
229Kd: 0.0086 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 269.212α = 90.00
b = 51.875β = 90.44
c = 129.069γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description