3K8O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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 U S A 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA [auth E], B [auth Q], C [auth S], D [auth T], E [auth U], F [auth Y]289Homo sapiensMutation(s): 1 
Gene Names: NPPNP
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Explore P00491 
Go to UniProtKB:  P00491
NIH Common Fund Data Resources
PHAROS:  P00491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
229
Query on 229

Download Ideal Coordinates CCD File 
BA [auth Y], J [auth E], N [auth Q], R [auth S], U [auth T], Y [auth U]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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth Y] , G [auth E] , H [auth E] , I [auth E] , K [auth Q] , L [auth Q] , M [auth Q] , O [auth S] , 
AA [auth Y],  G [auth E],  H [auth E],  I [auth E],  K [auth Q],  L [auth Q],  M [auth Q],  O [auth S],  P [auth S],  Q [auth S],  S [auth T],  T,  V [auth U],  W [auth U],  X [auth U],  Z [auth Y]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
229Ki:  8.600000381469727   nM  BindingDB
229Ki:  780   nM  BindingDB
229Kd:  0.009999999776482582   nM  BindingDB
229Kd :  0.008600001223385334   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.212α = 90
b = 51.875β = 90.44
c = 129.069γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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