4X8G

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK199

• PDB DOI: https://doi.org/10.2210/pdb4X8G/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2014-12-10 Released: 2015-01-28 
• Deposition Author(s): Lewis, H.D., Bax, B.D., Chung, C.-W., Polyakova, O., Thorpe, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation.

Lewis, H.D., Liddle, J., Coote, J.E., Atkinson, S.J., Barker, M.D., Bax, B.D., Bicker, K.L., Bingham, R.P., Campbell, M., Chen, Y.H., Chung, C.W., Craggs, P.D., Davis, R.P., Eberhard, D., Joberty, G., Lind, K.E., Locke, K., Maller, C., Martinod, K., Patten, C., Polyakova, O., Rise, C.E., Rudiger, M., Sheppard, R.J., Slade, D.J., Thomas, P., Thorpe, J., Yao, G., Drewes, G., Wagner, D.D., Thompson, P.R., Prinjha, R.K., Wilson, D.M.

(2015) Nat Chem Biol 11: 189-191

• PubMed: 25622091 
• DOI: https://doi.org/10.1038/nchembio.1735
• Primary Citation of Related Structures:  
  4X8C, 4X8G


• PubMed Abstract: 
  

  PAD4 has been strongly implicated in the pathogenesis of autoimmune, cardiovascular and oncological diseases through clinical genetics and gene disruption in mice. New selective PAD4 inhibitors binding a calcium-deficient form of the PAD4 enzyme have validated the critical enzymatic role of human and mouse PAD4 in both histone citrullination and neutrophil extracellular trap formation for, to our knowledge, the first time. The therapeutic potential of PAD4 inhibitors can now be explored.

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Organizational Affiliation: 

EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 75.51 kDa 
• Atom Count: 4,562 
• Modelled Residue Count: 606 
• Deposited Residue Count: 671 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-arginine deiminase type-4	A	671	Homo sapiens	Mutation(s): 1  Gene Names: PADI4, PADI5, PDI5 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3Z0	F [auth A]	[(3R)-3-aminopiperidin-1-yl][2-(1-ethyl-1H-pyrrolo[2,3-b]pyridin-2-yl)-7-methoxy-1-methyl-1H-benzimidazol-5-yl]methanone C24 H28 N6 O2 JCCVZBCVMBEDEN-QGZVFWFLSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.99	α = 90
b = 62.25	β = 124.71
c = 116.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
BUSTER	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Lewis, H.D., Bax, B.D., Chung, C.-W., Polyakova, O., Thorpe, J.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Database references
• Version 1.2: 2015-02-25
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Data collection, Derived calculations, Refinement description, Source and taxonomy
• Version 1.4: 2018-04-18
  Changes: Data collection
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references, Derived calculations