5C11

Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide


Experimental Data Snapshot

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

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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5A
A
52Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
H3 peptide
B
10Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4WQ
Query on 4WQ
B
L-peptide linkingC10 H21 N O2ALA
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 = 108.910α = 90.00
b = 108.910β = 90.00
c = 108.910γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data collection
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China programChina3127076

Revision History 

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