3BGS

Structure of human purine nucleoside phosphorylase with L-DADMe-ImmH and phosphate

• PDB DOI: https://doi.org/10.2210/pdb3BGS/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-27 Released: 2008-01-08 
• Deposition Author(s): Murkin, A.S., Ramagopal, U.A., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase

Rinaldo-Matthis, A., Murkin, A.S., Ramagopal, U.A., Clinch, K., Mee, S.P., Evans, G.B., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

(2008) J Am Chem Soc 130: 842-844

• PubMed: 18154341 
• DOI: https://doi.org/10.1021/ja710733g
• Primary Citation of Related Structures:  
  2Q7O, 3BGS


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,434 
• Modelled Residue Count: 286 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
purine nucleoside phosphorylase	A	289	Homo sapiens	Mutation(s): 1  Gene Names: NP, PNP 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIH	E [auth A]	7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one C12 H17 N4 O3 AFNHHLILYQEHKK-BDAKNGLRSA-O
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
DIH	PDBBind:  3BGS	Ki: 0.38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.801	α = 90
b = 142.801	β = 90
c = 167.348	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Murkin, A.S., Ramagopal, U.A., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 2.0: 2018-12-12
  Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description