1PFB

Structural Basis for specific binding of polycomb chromodomain to histone H3 methylated at K27

Structural Biology Knowledgebase: 1PFB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 1PFB

Classification: PEPTIDE BINDING PROTEIN

Total Structure Weight: 8174.41

Macromolecule Entities
Molecule Chains Length Organism Details
Polycomb protein A 55 Drosophila melanogaster Fragment: chromodomain
Gene Name(s): Pc CG7618
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H3, embryonic B 11 Strongylocentrotus purpuratus Mutation: K27X
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BME
Query on BME

A BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
M3L
Query on M3L
B L-PEPTIDE LINKING C9 H21 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.197
  • Space Group: I 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 32.43 α = 90.00
b = 77.03 β = 90.00
c = 77.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-24
  • Released Date: 2003-10-07
  • Deposition author(s): Min, J.R., Zhang, Y., Xu, R.-M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4