2YYR | pdb_00002yyr

Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide

• PDB DOI: https://doi.org/10.2210/pdb2YYR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2007-05-01 Released: 2008-05-06 
• Deposition Author(s): Nakamura, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.234 (Depositor) 
• R-Value Work: 
  0.213 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide

Nakamura, Y., Umehara, T., Padmanabhan, B., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 15.9 kDa 
• Atom Count: 1,015 
• Modeled Residue Count: 126 
• Deposited Residue Count: 142 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pygopus homolog 1	A, B	67	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9D0P5 (Mus musculus) Explore Q9D0P5  Go to UniProtKB:  Q9D0P5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K4Me3 peptide	C [auth P]	8	N/A	Mutation(s): 0

Small Molecules

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

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
M3L	C [auth P]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.234 (Depositor) 
• R-Value Work:  0.213 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.518	α = 90
b = 59.518	β = 90
c = 95.853	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Nakamura, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection