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


Ligand Structure Quality Assessment 


This is version 1.3 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase289Homo sapiensMutation(s): 1 
Gene Names: NPPNP
EC: 2.4.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00491 (Homo sapiens)
Explore P00491 
Go to UniProtKB:  P00491
PHAROS:  P00491
GTEx:  ENSG00000198805 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00491
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],
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],
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
Binding Affinity Annotations 
IDSourceBinding Affinity
229 BindingDB:  3K8O Ki: min: 8.6, max: 780 (nM) from 2 assay(s)
Kd: 8.60e-3 (nM) from 1 assay(s)
PDBBind:  3K8O Kd: 8.60e-3 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 



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
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations