Download MendeleyCrystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide
Huang, J., Li, H.(2015) Nat Commun
5C11
Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide
- PDB DOI: https://doi.org/10.2210/pdb5C11/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-06-12 Released: 2015-11-25
- Funding Organization(s): National Natural Science Foundation of China program
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.279
- R-Value Work: 0.245
- R-Value Observed: 0.248
Starting Model: experimental
View more details
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 |
| Lysine-specific demethylase 5A | 52 | Homo sapiens | Mutation(s): 0 Gene Names: KDM5A, JARID1A, RBBP2, RBP2 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P29375 (Homo sapiens) Explore P29375 Go to UniProtKB: P29375 | |||||
PHAROS: P29375 GTEx: ENSG00000073614 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P29375 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| H3 peptide | 10 | synthetic construct | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431 | |||||
PHAROS: P68431 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P68431 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | C [auth A], D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 4WQ Query on 4WQ | B | L-PEPTIDE LINKING | C10 H21 N O2 |  | ALA |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.279
- R-Value Work: 0.245
- R-Value Observed: 0.248
- Space Group: I 4 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 108.91 | α = 90 |
| b = 108.91 | β = 90 |
| c = 108.91 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| HKL-2000 | data scaling |
| MOLREP | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China program | China | 3127076 |
Revision History (Full details and data files)
- Version 1.0: 2015-11-25
Type: Initial release - Version 1.1: 2017-09-27
Changes: Data collection, Derived calculations - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2023-11-15
Changes: Data collection
