3C6W | pdb_00003c6w

Crystal structure of the ING5 PHD finger in complex with H3K4me3 peptide

• PDB DOI: https://doi.org/10.2210/pdb3C6W/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-05 Released: 2008-06-03 
• Deposition Author(s): Champagne, K.S., Pena, P.V., Johnson, K., Kutateladze, T.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.199 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

The crystal structure of the ING5 PHD finger in complex with an H3K4me3 histone peptide.

Champagne, K.S., Saksouk, N., Pena, P.V., Johnson, K., Ullah, M., Yang, X.J., Cote, J., Kutateladze, T.G.

(2008) Proteins 72: 1371-1376

• PubMed: 18623064 
• DOI: https://doi.org/10.1002/prot.22140
• Primary Citation of Related Structures:  
  3C6W

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Organizational Affiliation: 
• Department of Pharmacology, University of Colorado at Denver, Aurora, Colorado 80045, USA. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.55 kDa 
• Atom Count: 1,116 
• Modeled Residue Count: 121 
• Deposited Residue Count: 142 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor of growth protein 5	A, C	59	Homo sapiens	Mutation(s): 0  Gene Names: ING5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WYH8 (Homo sapiens) Explore Q8WYH8  Go to UniProtKB:  Q8WYH8
PHAROS:  Q8WYH8 GTEx:  ENSG00000168395

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K4me3 histone peptide	B, D	12	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth C], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B, D	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.199 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.14	α = 90
b = 68.14	β = 90
c = 28.25	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Champagne, K.S., Pena, P.V., Johnson, K., Kutateladze, T.G.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary