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 

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Ligand Structure Quality Assessment 


This is version 1.4 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
MoleculeChains Sequence 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / 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
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
Binding Affinity Annotations 
IDSourceBinding Affinity
229 BindingDB:  3K8O Ki: min: 9.00e-3, max: 0.78 (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
  • Version 1.4: 2024-02-21
    Changes: Data collection