Download MendeleyCrystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol
Johansson, C., Newman, J.A., Kawamura, A., Schofield, C.J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.To be published.
6RBI
Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol
- PDB DOI: https://doi.org/10.2210/pdb6RBI/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2019-04-10 Released: 2020-05-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.21 Å
- R-Value Free: 0.201
- R-Value Work: 0.184
- R-Value Observed: 0.185
Starting Model: experimental
View more details
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lysine-specific demethylase 5B,Lysine-specific demethylase 5B | 481 | Homo sapiens | Mutation(s): 0 Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UGL1 (Homo sapiens) Go to UniProtKB: Q9UGL1 | |||||
PHAROS: Q9UGL1 GTEx: ENSG00000117139 | |||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| JX8 (Subject of Investigation/LOI) Query on JX8 | F [auth A] | 5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol C10 H7 N5 O COSOIVLLWHGBPW-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | D [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| ZN Query on ZN | B [auth A], J [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], G [auth A], H [auth A], I [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MN Query on MN | C [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| NA Query on NA | K [auth A], L [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.21 Å
- R-Value Free: 0.201
- R-Value Work: 0.184
- R-Value Observed: 0.185
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 142.15 | α = 90 |
| b = 142.15 | β = 90 |
| c = 151.54 | γ = 120 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2020-05-13 Deposition Author(s): Johansson, C., Newman, J.A., Kawamura, A., Schofield, C.J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.
Revision History (Full details and data files)
- Version 1.0: 2020-05-13
Type: Initial release - Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
