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.

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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 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4CT	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

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

Entry History 

Deposition Data

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

Revision History  

• 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