2DW5

Crystal structure of human peptidylarginine deiminase 4 in complex with N-alpha-benzoyl-N5-(2-fluoro-1-iminoethyl)-L-ornithine amide

Structural Biology Knowledgebase: 2DW5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2DW5

Classification: HYDROLASE

Total Structure Weight: 75731.51

Macromolecule Entities
Molecule Chains Length Organism Details
Protein-arginine deiminase type-4 A 671 Homo sapiens EC#: 3.5.3.15 IUBMB
Gene Name(s): PADI4 Gene View PAD4 PADI5 PDI5

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

A N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE
(S)-N-ALPHA-BENZOYL-N5-(2-FLUORO-1-IMINOETHYL)- L-ORNITHINE AMIDE (Synonym)
C14 H20 N4 O2
LWFFSSMDFWZNNW-LBPRGKRZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.198
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 146.26 α = 90.00
b = 60.52 β = 124.19
c = 114.91 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-08-04
  • Released Date: 2006-10-17
  • Deposition author(s): Luo, Y., Arita, K., Sato, M., Thompson, P.R.

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