MolNFT v1 · #26045 · protein

Crystal structure of human peptidylarginine deiminase TYPE4 (PAD4) in complex with benzoyl-L-arginine amide

1WDA · Protein-arginine deiminase type IV: “Crystal structure of human peptidylarginine deiminase TYPE4 (PAD4) in complex with benzoyl-L-arginine amide”. X-ray diffraction, 3 ligands (BAG, CA, SO4), 2 pockets (best druggability 0.55).…

PDB: 1WDA
Type: protein
Length: 628 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-arginine deiminase type IV
EC: 3.5.3.15
UniProt: Q9UM07
Ligands: BAG, CA, SO4
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein-arginine deiminase type IV (EC 3.5.3.15)	protein	628	21% helix, 36% strand	Q9UM07

Ligands and binding sites

BAG · N-[(E)-2-amino-1-(3-{[amino(imino)methyl]amino}propyl)-2-hydroxyvinyl]benzamide · ligand · chains A
CA · Calcium ion · metal · 5 copies · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	160	0.55	0.81	29	BAG
2	61	0.30	0.75	17	empty

Compared structures

1WDA · Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Q9UM07 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-4 (Q9UM07) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9UM07
Elsewhere: RCSB PDB 1WDA · PDBe 1WDA · UniProt Q9UM07

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