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
6NFL
Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G complexed with 2-HP
- PDB DOI: https://doi.org/10.2210/pdb6NFL/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: 1.73 Å
- R-Value Free: 0.194
- R-Value Work: 0.162
- R-Value Observed: 0.164
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.3 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): 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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UH17 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| L60 Query on L60 | B [auth A] | 1,3-diazinan-2-one C4 H8 N2 O NQPJDJVGBDHCAD-UHFFFAOYSA-N |  | ||
| 71O Query on 71O | C [auth A] | pyrimidin-2-ol C4 H4 N2 O VTGOHKSTWXHQJK-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], F [auth A], G [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.73 Å
- R-Value Free: 0.194
- R-Value Work: 0.162
- R-Value Observed: 0.164
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.65 | α = 90 |
| b = 50.65 | β = 90 |
| c = 149.25 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
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 - Version 1.3: 2024-10-16
Changes: Structure summary
