5C11 | pdb_00005c11

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 
• 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: 2.80 Å
• R-Value Free: 
  0.279 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide

Huang, J., Li, H.

(2015) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 7.12 kDa 
• Atom Count: 457 
• Modeled Residue Count: 59 
• Deposited Residue Count: 62 
• Unique protein chains: 2

Macromolecules

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)
UniProt & NIH Common Fund Data Resources
Find proteins for P29375 (Homo sapiens) Explore P29375  Go to UniProtKB:  P29375
PHAROS:  P29375 GTEx:  ENSG00000073614

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3 peptide	B	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 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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	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 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• 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
  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