6NFM

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2018-12-20 Released: 2019-12-25 
  • Deposition Author(s): Shi, K., Aihara, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history. 


Literature

Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B

Shi, K., Demir, O., Carpenter, M.A., Banerjee, S., Harki, D.A., Amaro, R.E., Harris, R.S., Aihara, H.

(2020) FASEB Bioadv 2: 49-58


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA dC->dU-editing enzyme APOBEC-3B193Homo sapiensMutation(s): 11 
Gene Names: APOBEC3B
EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UH17 (Homo sapiens)
Explore Q9UH17 
Go to UniProtKB:  Q9UH17
PHAROS:  Q9UH17
GTEx:  ENSG00000179750 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UH17
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.314α = 90
b = 50.314β = 90
c = 149.808γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description