Download MendeleyCrystal structure of human JARID1B in complex with S40563a
srikannathasan, v.To be published.
5LW9
Crystal structure of human JARID1B in complex with S40563a
- PDB DOI: https://doi.org/10.2210/pdb5LW9/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2016-09-15 Released: 2016-09-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.218
- R-Value Work: 0.185
- R-Value Observed: 0.186
Starting Model: experimental
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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 |
| Lysine-specific demethylase 5B,Lysine-specific demethylase 5B | 481 | Homo sapiens | Mutation(s): 0 Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UGL1 (Homo sapiens) Explore Q9UGL1 Go to UniProtKB: Q9UGL1 | |||||
PHAROS: Q9UGL1 GTEx: ENSG00000117139 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UGL1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 5UJ Query on 5UJ | I [auth A] | 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one C23 H22 Cl2 N6 O RLRGPZGIQMEBLC-UHFFFAOYSA-N |  | ||
| DMS Query on DMS | F [auth A], G [auth A], H [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | D [auth A], E [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MN Query on MN | C [auth A], J [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.218
- R-Value Work: 0.185
- R-Value Observed: 0.186
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 142.96 | α = 90 |
| b = 142.96 | β = 90 |
| c = 152.47 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| MOLREP | data collection |
| PDB_EXTRACT | data extraction |
| xia2 | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-09-28 Deposition Author(s): Srikannathasan, V., Le Bihan, Y.V., Szykowska, A., Johansson, C., Gileadi, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.
Revision History (Full details and data files)
- Version 1.0: 2016-09-28
Type: Initial release - Version 1.1: 2019-10-16
Changes: Data collection - Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description - Version 1.3: 2024-11-06
Changes: Structure summary
