Macromolecule Content

Total Structure Weight: 7.12 kDa
Atom Count: 457
Residue Count: 59
Unique protein chains: 2

5C11

Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide

DOI: 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
Deposition Author(s): Huang, J., Li, H.
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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide

Huang, J., Li, H.

(2015) Nat Commun

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5A	A	52	Homo sapiens	Mutation(s): 0 Gene Names: KDM5A, JARID1A, RBBP2, RBP2 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for P29375 (Homo sapiens) Explore P29375 Go to UniProtKB: P29375
NIH Common Fund Data Resources
PHAROS P29375 GTEx ENSG00000073614
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3 peptide	B	10	synthetic construct	Mutation(s): 0
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
NIH Common Fund Data Resources
PHAROS P68431 GTEx ENSG00000197409GTEx ENSG00000197153GTEx ENSG00000278828GTEx ENSG00000275714GTEx ENSG00000273983GTEx ENSG00000274750GTEx ENSG00000275379GTEx ENSG00000277775
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] MOL2 format, chain C [A] MOL2 format, chain D [A]	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

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 Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2015-06-12
Released Date: 2015-11-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China program	China	3127076

Revision History

Version 1.0: 2015-11-25
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection, Derived calculations

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.