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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

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

Find similar proteins by:

(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]	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
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
229 Query on 229 Download Ideal Coordinates CCD File SDF format, chain BA [auth Y] SDF format, chain J [auth E] SDF format, chain N [auth Q] SDF format, chain R [auth S] SDF format, chain U [auth T] SDF format, chain Y [auth U] MOL2 format, chain BA [auth Y] MOL2 format, chain J [auth E] MOL2 format, chain N [auth Q] MOL2 format, chain R [auth S] MOL2 format, chain U [auth T] MOL2 format, chain Y [auth U]	BA [auth Y] J [auth E] N [auth Q] R [auth S] U [auth T] 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		Interactions Focus chain BA [auth Y] Focus chain J [auth E] Focus chain N [auth Q] Focus chain R [auth S] Focus chain U [auth T] Focus chain Y [auth U] Interactions & Density Focus chain BA [auth Y] Focus chain J [auth E] Focus chain N [auth Q] Focus chain R [auth S] Focus chain U [auth T] Focus chain Y [auth U]
SO4 Query on SO4 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 Q] SDF format, chain P [auth S] SDF format, chain Q [auth S] SDF format, chain T SDF format, chain V [auth U] SDF format, chain X [auth U] SDF format, chain AA [auth Y] SDF format, chain G [auth E] SDF format, chain I [auth E] SDF format, chain O [auth S] SDF format, chain S [auth T] SDF format, chain W [auth U] SDF format, chain Z [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 Q] MOL2 format, chain P [auth S] MOL2 format, chain Q [auth S] MOL2 format, chain T MOL2 format, chain V [auth U] MOL2 format, chain X [auth U] MOL2 format, chain AA [auth Y] MOL2 format, chain G [auth E] MOL2 format, chain I [auth E] MOL2 format, chain O [auth S] MOL2 format, chain S [auth T] MOL2 format, chain W [auth U] MOL2 format, chain Z [auth Y]	AA [auth Y] G [auth E] H [auth E] I [auth E] K [auth Q] 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		Interactions Focus chain AA [auth Y] Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Focus chain K [auth Q] Focus chain L [auth Q] Focus chain M [auth Q] Focus chain O [auth S] Focus chain P [auth S] Focus chain Q [auth S] Focus chain S [auth T] Focus chain T Focus chain V [auth U] Focus chain W [auth U] Focus chain X [auth U] Focus chain Z [auth Y] Interactions & Density Focus chain AA [auth Y] Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Focus chain K [auth Q] Focus chain L [auth Q] Focus chain M [auth Q] Focus chain O [auth S] Focus chain P [auth S] Focus chain Q [auth S] Focus chain S [auth T] Focus chain T Focus chain V [auth U] Focus chain W [auth U] Focus chain X [auth U] Focus chain Z [auth Y]

Binding Affinity Annotations
ID	Source	Binding Affinity
229	BindingDB: 3K8O	Ki: min: 8.6, max: 780 (nM) from 2 assay(s)
	BindingDB: 3K8O	Kd: 8.60e-3 (nM) from 1 assay(s)
	PDBBind: 3K8O	Kd: 8.60e-3 (nM) from 1 assay(s)