3OZD

Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pCl-phenylthioDADMeImmA

PDB DOI: https://doi.org/10.2210/pdb3OZD/pdb

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

Deposited: 2010-09-24 Released: 2011-09-28
Deposition Author(s): Ho, M., Guan, R., Almo, S.C., Schramm, V.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257
R-Value Work: 0.200
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase

Ho, M., Guan, R., Almo, S.C., Schramm, V.L.

To be published.

Macromolecule Content

Total Structure Weight: 63.33 kDa
Atom Count: 4,398
Modelled Residue Count: 546
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-methyl-5'-thioadenosine phosphorylase	A, B	283	Homo sapiens	Mutation(s): 0 Gene Names: MTAP, MSAP EC: 2.4.2.28
UniProt & NIH Common Fund Data Resources
Find proteins for Q13126 (Homo sapiens) Explore Q13126 Go to UniProtKB: Q13126
PHAROS: Q13126 GTEx: ENSG00000099810
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13126
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4CT Query on 4CT Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A]	C [auth A], D [auth B]	(3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol C₁₈ H₂₀ Cl N₅ O S MZZBHZOHYGEGEE-DOMZBBRYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
4CT	BindingDB: 3OZD	Kd: 1.00e-2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257
R-Value Work: 0.200
R-Value Observed: 0.202
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.539	α = 90
b = 121.539	β = 90
c = 87.661	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-28
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.