3PHB

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

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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 DADMe-ImmG

Ho, M.Cassera, M.B.Murkin, A.S.Almo, S.C.Schramm, V.L.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase324Homo sapiensMutation(s): 0 
Gene Names: PNPNP
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
IM5
Query on IM5

Download Ideal Coordinates CCD File 
G [auth E]
J [auth Q]
N [auth S]
Q [auth T]
S [auth U]
G [auth E],
J [auth Q],
N [auth S],
Q [auth T],
S [auth U],
W [auth Y]
2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
C12 H17 N5 O3
GSPTUGDLYPMLCQ-SFYZADRCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth E]
I [auth E]
K [auth Q]
L [auth Q]
M [auth S]
H [auth E],
I [auth E],
K [auth Q],
L [auth Q],
M [auth S],
O [auth S],
P [auth T],
R [auth T],
T [auth U],
U [auth Y],
V [auth Y],
X [auth Y]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Binding Affinity Annotations 
IDSourceBinding Affinity
IM5 BindingDB:  3PHB Ki: min: 7.00e-3, max: 0.16 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.27α = 90
b = 52.632β = 90.33
c = 128.119γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Non-polymer description
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations