3K8Q

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

• PDB DOI: https://doi.org/10.2210/pdb3K8Q/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., Almo, S.C., Scharmm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.262 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Crystal structure of human nucleoside phosphorylase in complex with SerMe-ImmH

Ho, M., Almo, S.C., Scharmm, 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)

Macromolecule Content

• Total Structure Weight: 32.61 kDa 
• Atom Count: 2,305 
• 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
22A	B [auth A]	7-({[2-hydroxy-1-(hydroxymethyl)ethyl]amino}methyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one C10 H14 N4 O3 YGATXRRSBPFSBK-UHFFFAOYSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
22A	BindingDB:  3K8Q	Ki: min: 5.20e-3, max: 5.2 (nM) from 3 assay(s)
		ΔH: -8.46e+1 (kJ/mol) from 1 assay(s)
		ΔG: -6.49e+1 (kJ/mol) from 1 assay(s)
	PDBBind:  3K8Q	Kd: 5.20e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.262 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.968	α = 90
b = 142.968	β = 90
c = 168.548	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Ho, M., Almo, S.C., Scharmm, V.L.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: 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