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Download EndnoteCrystal structure of KDM5B in complex with KDOPZ000049a.
srikannathasan, v.To be published.
6EJ0
Crystal structure of KDM5B in complex with KDOPZ000049a.
- DOI: 10.2210/pdb6EJ0/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2017-09-19 Released: 2018-05-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.06 Å
- R-Value Free: 0.210
- R-Value Work: 0.190
- R-Value Observed: 0.191
wwPDB Validation 3D Report Full Report
Literature
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Lysine-specific demethylase 5B,Lysine-specific demethylase 5B | A | 458 | Homo sapiens | Mutation(s): 0 Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt) |
Find proteins for Q9UGL1 (Homo sapiens) Go to UniProtKB: Q9UGL1 | ||||
NIH Common Fund Data Resources | ||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| B7K Query on B7K | A | 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile C21 H23 N7 O2 KGLWYCXNVRPKIE-SFHVURJKSA-N |  | Ligand Interaction | |
| DMS Query on DMS | A | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | Ligand Interaction | |
| ZN Query on ZN | A | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | Ligand Interaction | |
| EDO Query on EDO | A | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| MN Query on MN | A | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.06 Å
- R-Value Free: 0.210
- R-Value Work: 0.190
- R-Value Observed: 0.191
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 141.82 | α = 90 |
| b = 141.82 | β = 90 |
| c = 151.75 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| xia2 | data reduction |
| xia2 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Deposited Date: 2017-09-19
- Released Date: 2018-05-02 Deposition Author(s): Srikannathasan, V., Newman, J.A., Szykowska, A., Wright, M., Ruda, G.F., Vazquez-Rodriguez, S.A., Kupinska, K., Strain-Damerell, C., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Huber, K., von Delft, F.
