3K8Q | pdb_00003k8q

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.222 (Depositor), 0.224 (DCC)
R-Value Observed:
0.224 (Depositor)

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Ligand Structure Quality Assessment

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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

Macromolecule Content

Total Structure Weight: 32.61 kDa
Atom Count: 2,305
Modeled Residue Count: 286
Deposited Residue Count: 289
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00491
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
22A Query on 22A Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.222 (Depositor), 0.224 (DCC)
R-Value Observed: 0.224 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2010-03-02

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.