Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7123.72 
• Atom Count: 457 
• Residue Count: 62 
• 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
• Expression System: Escherichia coli BL21(DE3)


• 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 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.803 Å
• R-Value Free: 0.279 
• R-Value Work: 0.245 

Literature

Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide

Huang, J., Li, H.

(2015) Nat Commun --: --

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysine-specific demethylase 5A	A	52	Homo sapiens	Mutation(s): 0  Gene Names: KDM5A (JARID1A, RBBP2, RBP2) EC: 1.14.11.-
Find proteins for P29375 (Homo sapiens) Go to Gene View: KDM5A Go to UniProtKB:  P29375

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
H3 peptide	B	10	Homo sapiens	Mutation(s): 0  Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens) Go to UniProtKB:  P68431

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4WQ	B	L-peptide linking	C10 H21 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.803 Å
• R-Value Free: 0.279 
• R-Value Work: 0.245 
• Space Group: I 4 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 108.910	α = 90.00
b = 108.910	β = 90.00
c = 108.910	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-12 
• Released Date: 2015-11-25 
• Deposition Author(s): Huang, J., Li, H.

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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
  Type: Data collection, Derived calculations