1PF7

CRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH IMMUCILLIN H

Structural Biology Knowledgebase: 1PF7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 1PF7

Classification: TRANSFERASE

Total Structure Weight: 32739.52

Macromolecule Entities
Molecule Chains Length Organism Details
PURINE NUCLEOSIDE PHOSPHORYLASE E 289 Homo sapiens EC#: 2.4.2.1 IUBMB
Details: complexed with IMMUCILLIN H, residue IMH
Gene Name(s): PNP Gene View NP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

E 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN- 9-YL)-D-RIBITOL
C11 H14 N4 O4
IWKXDMQDITUYRK-KUBHLMPHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

E SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IMH IC50: 3.5 - 100 nM (99) BindingDB
Kd: 0.023 - 0.058 nM (88 - 99) BindingDB
Ki: 0.056 - 56 nM (88 - 99) BindingDB

N/A in BindingMoad
Ki: 0.072 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.200
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 139.39 α = 90.00
b = 139.39 β = 90.00
c = 161.31 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-24
  • Released Date: 2004-06-01
  • Deposition author(s): De Azevedo Jr., W.F., Canduri, F., Dos Santos, D.M., Pereira, J.H., Dias, M.V.B., Silva, R.G., Mendes, M.A., Palma, M.S., Basso, L.A., Santos, D.S.

Revision History

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