Download MendeleyActive 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
6NFK
Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G bound to iodide
- PDB DOI: https://doi.org/10.2210/pdb6NFK/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2018-12-20 Released: 2019-12-25
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.238
- R-Value Work: 0.189
- R-Value Observed: 0.191
wwPDB Validation 3D Report Full Report
Currently 6NFK does not have a validation slider image.
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA dC->dU-editing enzyme APOBEC-3B | 193 | Homo sapiens | Mutation(s): 12 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 | |||||
Find proteins for Q9HC16 (Homo sapiens) Explore Q9HC16 Go to UniProtKB: Q9HC16 | |||||
PHAROS: Q9HC16 GTEx: ENSG00000239713 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | Q9UH17Q9HC16 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IOD Query on IOD | E [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M |  | ||
| EDO Query on EDO | B [auth A], C [auth A], D [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.238
- R-Value Work: 0.189
- R-Value Observed: 0.191
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.6 | α = 90 |
| b = 50.6 | β = 90 |
| c = 149.3 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Structure Validation
Currently 6NFK does not have a validation slider image.
Entry History & Funding Information
Deposition Data
- Released Date: 2019-12-25 Deposition Author(s): Shi, K., Orellana, K., Aihara, H.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM118047 |
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
