3PHB

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG

PDB DOI: https://doi.org/10.2210/pdb3PHB/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-11-03 Released: 2011-11-09
Deposition Author(s): Ho, M., Cassera, M.B., Murkin, A.S., Almo, S.C., Schramm, V.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.295
R-Value Work: 0.230
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG

Ho, M., Cassera, M.B., Murkin, A.S., Almo, S.C., Schramm, V.L.

To be published.

Macromolecule Content

Total Structure Weight: 219.7 kDa
Atom Count: 13,732
Modelled Residue Count: 1,718
Deposited Residue Count: 1,944
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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] A [auth E], B [auth Q], C [auth S], D [auth T], E [auth U], F [auth Y]	324	Homo sapiens	Mutation(s): 0 Gene Names: PNP, NP 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00491
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IM5 Query on IM5 Download Ideal Coordinates CCD File SDF format, chain J [auth Q] SDF format, chain N [auth S] SDF format, chain Q [auth T] SDF format, chain W [auth Y] SDF format, chain G [auth E] SDF format, chain S [auth U] MOL2 format, chain J [auth Q] MOL2 format, chain N [auth S] MOL2 format, chain Q [auth T] MOL2 format, chain W [auth Y] MOL2 format, chain G [auth E] MOL2 format, chain S [auth U]	G [auth E] J [auth Q] N [auth S] Q [auth T] S [auth U] G [auth E], J [auth Q], N [auth S], Q [auth T], S [auth U], W [auth Y]	2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one C₁₂ H₁₇ N₅ O₃ GSPTUGDLYPMLCQ-SFYZADRCSA-N		Interactions Focus chain G [auth E] Focus chain J [auth Q] Focus chain N [auth S] Focus chain Q [auth T] Focus chain S [auth U] Focus chain W [auth Y] Interactions & Density Focus chain G [auth E] Focus chain J [auth Q] Focus chain N [auth S] Focus chain Q [auth T] Focus chain S [auth U] Focus chain W [auth Y]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain K [auth Q] SDF format, chain L [auth Q] SDF format, chain M [auth S] SDF format, chain P [auth T] SDF format, chain R [auth T] SDF format, chain T [auth U] SDF format, chain U [auth Y] SDF format, chain X [auth Y] SDF format, chain I [auth E] SDF format, chain O [auth S] SDF format, chain V [auth Y] MOL2 format, chain H [auth E] MOL2 format, chain K [auth Q] MOL2 format, chain L [auth Q] MOL2 format, chain M [auth S] MOL2 format, chain P [auth T] MOL2 format, chain R [auth T] MOL2 format, chain T [auth U] MOL2 format, chain U [auth Y] MOL2 format, chain X [auth Y] MOL2 format, chain I [auth E] MOL2 format, chain O [auth S] MOL2 format, chain V [auth Y]	H [auth E] I [auth E] K [auth Q] L [auth Q] M [auth S] H [auth E], I [auth E], K [auth Q], L [auth Q], M [auth S], O [auth S], P [auth T], R [auth T], T [auth U], U [auth Y], V [auth Y], X [auth Y]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth E] Focus chain I [auth E] Focus chain K [auth Q] Focus chain L [auth Q] Focus chain M [auth S] Focus chain O [auth S] Focus chain P [auth T] Focus chain R [auth T] Focus chain T [auth U] Focus chain U [auth Y] Focus chain V [auth Y] Focus chain X [auth Y] Interactions & Density Focus chain H [auth E] Focus chain I [auth E] Focus chain K [auth Q] Focus chain L [auth Q] Focus chain M [auth S] Focus chain O [auth S] Focus chain P [auth T] Focus chain R [auth T] Focus chain T [auth U] Focus chain U [auth Y] Focus chain V [auth Y] Focus chain X [auth Y]

Binding Affinity Annotations
ID	Source	Binding Affinity
IM5	BindingDB: 3PHB	Ki: min: 0.16, max: 7 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.295
R-Value Work: 0.230
R-Value Observed: 0.233
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 269.27	α = 90
b = 52.632	β = 90.33
c = 128.119	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2011-12-14
Changes: Non-polymer description
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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Help and Resources

3PHB

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG

Crystal Structure of human purine nucleoside phosphorylase in complex with DADMe-ImmG

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)