2DEY

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3

Structural Biology Knowledgebase: 2DEY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DEY

Classification: HYDROLASE

Total Structure Weight: 76368.19

Macromolecule Entities
Molecule Chains Length Organism Details
Protein-arginine deiminase type IV X 671 Homo sapiens EC#: 3.5.3.15 IUBMB
Mutation: C645A
Gene Name(s): PADI4 Gene View PAD4 PADI5 PDI5
10-mer peptide from histone H4 A 11 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

X SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

X CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A NON-POLYMER C2 H4 O --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.199
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 146.19 α = 90.00
b = 60.61 β = 124.18
c = 115.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-18
  • Released Date: 2006-04-11
  • Deposition author(s): Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4