3K8O

Crystal structure of human purine nucleoside phosphorylase in complex with DATMe-ImmH

• PDB DOI: https://doi.org/10.2210/pdb3K8O/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-10-14 Released: 2010-03-02 
• Deposition Author(s): Ho, M., Rinaldo-matthis, A., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Crystal structure of human purine nucleoside phosphorylase in complex with DATMe-Immucillin H

Ho, M., Rinaldo-matthis, A., Almo, S.C., Schramm, V.L.

(2010) Proc Natl Acad Sci U S A 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 196.26 kDa 
• Atom Count: 13,632 
• Modelled Residue Count: 1,699 
• Deposited Residue Count: 1,734 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A [auth E], B [auth Q], C [auth S], D [auth T], E [auth U], F [auth Y]	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) Go to UniProtKB:  P00491
PHAROS:  P00491 GTEx:  ENSG00000198805

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
229	BA [auth Y], J [auth E], N [auth Q], R [auth S], U [auth T], Y [auth U]	7-({[(1R,2S)-2,3-DIHYDROXY-1-(HYDROXYMETHYL)PROPYL]AMINO}METHYL)-3,5-DIHYDRO-4H-PYRROLO[3,2-D]PYRIMIDIN-4-ONE C11 H16 N4 O4 CGYSFECPLYEOMH-HTQZYQBOSA-N
SO4	AA [auth Y], G [auth E], H [auth E], I [auth E], K [auth Q], L [auth Q], M [auth Q], O [auth S], P [auth S], Q [auth S], S [auth T], T, V [auth U], W [auth U], X [auth U], Z [auth Y]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
229	BindingDB:  3K8O	Ki: min: 9.00e-3, max: 0.78 (nM) from 2 assay(s)
		Kd: 8.60e-3 (nM) from 1 assay(s)
	PDBBind:  3K8O	Kd: 8.60e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 269.212	α = 90
b = 51.875	β = 90.44
c = 129.069	γ = 90

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: 2010-03-02 
Deposition Author(s): Ho, M., Rinaldo-matthis, A., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection