PDBsum entry 3bgs

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protein ligands links
Transferase PDB id
Protein chain
286 a.a. *
PO4 ×3
Waters ×101
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Structure of human purine nucleoside phosphorylase with l- dadme-immh and phosphate
Structure: Purine nucleoside phosphorylase. Chain: a. Synonym: inosine phosphorylase. Pnp. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Strain: bl21(de3). Gene: np, pnp. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.10Å     R-factor:   0.219     R-free:   0.249
Authors: A.S.Murkin,U.A.Ramagopal,S.C.Almo,V.L.Schramm
Key ref: A.Rinaldo-Matthis et al. (2008). L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase. J Am Chem Soc, 130, 842-844. PubMed id: 18154341
27-Nov-07     Release date:   08-Jan-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00491  (PNPH_HUMAN) -  Purine nucleoside phosphorylase
289 a.a.
286 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate
2. Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Purine nucleoside
Bound ligand (Het Group name = DIH)
matches with 48.00% similarity
Bound ligand (Het Group name = PO4)
corresponds exactly
= purine
+ alpha-D-ribose 1-phosphate
Purine deoxynucleoside
+ phosphate
= purine
+ 2'-deoxy-alpha-D-ribose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     small molecule metabolic process   16 terms 
  Biochemical function     catalytic activity     9 terms  


J Am Chem Soc 130:842-844 (2008)
PubMed id: 18154341  
L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase.
A.Rinaldo-Matthis, A.S.Murkin, U.A.Ramagopal, K.Clinch, S.P.Mee, G.B.Evans, P.C.Tyler, R.H.Furneaux, S.C.Almo, V.L.Schramm.
Human purine nucleoside phosphorylase (PNP) was crystallized with transition-state analogue inhibitors Immucillin-H and DADMe-Immucillin-H synthesized with ribosyl mimics of l-stereochemistry. The inhibitors demonstrate that major driving forces for tight binding of these analogues are the leaving group interaction and the cationic mimicry of the transition state, even though large geometric changes occur with d-Immucillins and l-Immucillins bound to human PNP.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19425594 A.A.Edwards, J.M.Mason, K.Clinch, P.C.Tyler, G.B.Evans, and V.L.Schramm (2009).
Altered enthalpy-entropy compensation in picomolar transition state analogues of human purine nucleoside phosphorylase.
  Biochemistry, 48, 5226-5238.  
19170524 K.Clinch, G.B.Evans, R.F.Fröhlich, R.H.Furneaux, P.M.Kelly, L.Legentil, A.S.Murkin, L.Li, V.L.Schramm, P.C.Tyler, and A.D.Woolhouse (2009).
Third-generation immucillins: syntheses and bioactivities of acyclic immucillin inhibitors of human purine nucleoside phosphorylase.
  J Med Chem, 52, 1126-1143.  
19778725 M.Ghanem, A.S.Murkin, and V.L.Schramm (2009).
Ribocation transition state capture and rebound in human purine nucleoside phosphorylase.
  Chem Biol, 16, 971-979.  
19191546 M.Ghanem, N.Zhadin, R.Callender, and V.L.Schramm (2009).
Loop-tryptophan human purine nucleoside phosphorylase reveals submillisecond protein dynamics.
  Biochemistry, 48, 3658-3668.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.