3OZE

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

PDB DOI: https://doi.org/10.2210/pdb3OZE/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: 2.00 ?
R-Value Free: 0.262
R-Value Work: 0.216
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

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: 188.23 kDa
Atom Count: 12,542
Modelled Residue Count: 1,584
Deposited Residue Count: 1,698
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, C, D, E A, B, C, D, E, F	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
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth E] mmCIF format, chain L [auth F]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.262
R-Value Work: 0.216
R-Value Observed: 0.218
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 79.517	α = 90
b = 81.81	β = 91
c = 130.282	γ = 90

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: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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3OZE

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)