3K8Q

Crystal structure of human purine nucleoside phosphorylase in complex with SerMe-Immucillin H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human nucleoside phosphorylase in complex with SerMe-ImmH

Ho, M.Almo, S.C.Scharmm, V.L.

(2010) Proc Natl Acad Sci U S A 


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
A
289Homo sapiensMutation(s): 1 
Gene Names: NPPNP
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Go to UniProtKB:  P00491
NIH Common Fund Data Resources
PHAROS  P00491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
22A
Query on 22A

Download CCD File 
A
7-({[2-hydroxy-1-(hydroxymethyl)ethyl]amino}methyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
C10 H14 N4 O3
YGATXRRSBPFSBK-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
22AΔG:  64.9000015258789   kJ/mol  BindingDB
22AKi:  0.10999999940395355   nM  BindingDB
22AKd :  0.005200000014156103   nM  PDBBind
22AKi:  5.199999809265137   nM  BindingDB
22AΔH:  84.5999984741211   kJ/mol  BindingDB
22AKi:  0.009999999776482582   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.968α = 90
b = 142.968β = 90
c = 168.548γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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