1WDA | pdb_00001wda

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural basis for Ca(2+)-induced activation of human PAD4

Arita, K.Hashimoto, H.Shimizu, T.Nakashima, K.Yamada, M.Sato, M.

(2004) Nat Struct Mol Biol 11: 777-783

  • DOI: https://doi.org/10.1038/nsmb799
  • Primary Citation Related Structures: 
    1WD8, 1WD9, 1WDA

  • PubMed Abstract: 

    Peptidylarginine deiminase 4 (PAD4) is a Ca(2+)-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. Its gene is a susceptibility locus for rheumatoid arthritis. Here we present the crystal structure of Ca(2+)-free wild-type PAD4, which shows that the polypeptide chain adopts an elongated fold in which the N-terminal domain forms two immunoglobulin-like subdomains, and the C-terminal domain forms an alpha/beta propeller structure. Five Ca(2+)-binding sites, none of which adopt an EF-hand motif, were identified in the structure of a Ca(2+)-bound inactive mutant with and without bound substrate. These structural data indicate that Ca(2+) binding induces conformational changes that generate the active site cleft. Our findings identify a novel mechanism for enzyme activation by Ca(2+) ions, and are important for understanding the mechanism of protein citrullination and for developing PAD-inhibiting drugs for the treatment of rheumatoid arthritis.


  • Organizational Affiliation
    • Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Macromolecule Content 

  • Total Structure Weight: 75.55 kDa 
  • Atom Count: 5,145 
  • Modeled Residue Count: 628 
  • Deposited Residue Count: 670 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein-arginine deiminase type IV670Homo sapiensMutation(s): 1 
EC: 3.5.3.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM07 (Homo sapiens)
Explore Q9UM07 
Go to UniProtKB:  Q9UM07
PHAROS:  Q9UM07
GTEx:  ENSG00000159339 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM07
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BAG

Query on BAG



Download:Ideal Coordinates CCD File
J [auth A]N-[(E)-2-AMINO-1-(3-{[AMINO(IMINO)METHYL]AMINO}PROPYL)-2-HYDROXYVINYL]BENZAMIDE
C13 H19 N5 O2
YRINIXCRGISJPA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.133α = 90
b = 60.045β = 124.23
c = 115.406γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-29
    Changes: Data collection