1RT9

Structure of human purine nucleoside phosphorylase in complex with Immucillin-H and sulfate

• PDB DOI: https://doi.org/10.2210/pdb1RT9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-10 Released: 2005-02-22 
• Deposition Author(s): Shi, W., Lewandowicz, A., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.251 
• R-Value Observed: 0.254 

Starting Model: experimental

Literature

Structural comparison of human and malarial purine nucleoside phosphorylases

Shi, W., Lewandowicz, A., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

To be published.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,282 
• Modelled Residue Count: 282 
• 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): 0  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
IMH	E [auth A]	1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL C11 H14 N4 O4 IWKXDMQDITUYRK-KUBHLMPHSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
IMH	BindingDB:  1RT9	Ki: min: 0.06, max: 72 (nM) from 6 assay(s)
		Kd: min: 0.02, max: 0.06 (nM) from 3 assay(s)
		IC50: min: 0.06, max: 100 (nM) from 3 assay(s)
		ΔH: -3.50e+1 (kJ/mol) from 1 assay(s)
		ΔG: -4.56e+1 (kJ/mol) from 1 assay(s)
	PDBBind:  1RT9	Ki: 0.06 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.281 
• R-Value Work: 0.251 
• R-Value Observed: 0.254 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.076	α = 90
b = 142.076	β = 90
c = 166.955	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Shi, W., Lewandowicz, A., Tyler, P.C., Furneaux, R.H., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2022-10-05
  Changes: Atomic model, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Refinement description