1RSZ

Structure of human purine nucleoside phosphorylase in complex with DADMe-Immucillin-H and sulfate

Structural Biology Knowledgebase: 1RSZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.250

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1RSZ

Classification: transferase

Total Structure Weight: 32740.57

Macromolecule Entities
Molecule Chains Length Organism Details
Purine nucleoside phosphorylase A 289 Homo sapiens EC#: 2.4.2.1 IUBMB
Gene Name(s): PNP Gene View NP

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DIH
Query on DIH

A 3-HYDROXY-4-HYDROXYMETHYL-1-(4-OXO-4,4A,5,7A- TETRAHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YLMETHYL)- PYRROLIDINIUM
(3R, (Synonym)
C12 H19 N4 O3
WFVGWLHAOKEIOJ-MFQSTILNSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DIH Kd: 0.0085 nM (99) BindingDB
Ki: 0.0107 - 8.5 nM (88 - 99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.250
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 142.16 α = 90.00
b = 142.16 β = 90.00
c = 166.39 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-12-10
  • Released Date: 2005-02-22
  • Deposition author(s): Shi, W., Lewandowicz, A., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4