3OZD | pdb_00003ozd

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 (Depositor), 0.260 (DCC)
R-Value Work:
0.200 (Depositor), 0.206 (DCC)
R-Value Observed:
0.202 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 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
Modeled Residue Count: 546
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF format, chain D [auth B] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257 (Depositor), 0.260 (DCC)
R-Value Work: 0.200 (Depositor), 0.206 (DCC)
R-Value Observed: 0.202 (Depositor)

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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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
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.