MolNFT v1 · #100600 · protein

Crystal structure of protein arginine deiminase 2 (1 mm CA2+)

4N28 · Protein-arginine deiminase type-2: “Crystal structure of protein arginine deiminase 2 (1 mm CA2+)”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.79). MolNFT v1 #100600 on GenesisL1: 3D structure, binding sites…

PDB: 4N28
Type: protein
Length: 659 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-arginine deiminase type-2
EC: 3.5.3.15
UniProt: Q9Y2J8
Ligands: CA
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein-arginine deiminase type-2 (EC 3.5.3.15)	protein	659	19% helix, 37% strand	Q9Y2J8

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

6 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	259	0.79	0.91	52	empty
2	52	0.43	0.83	15	empty
3	81	0.35	0.75	16	empty
4	67	0.35	0.76	17	MPD
5	72	0.33	0.76	16	empty

Compared structures

4N28 · Crystal structure of Protein Arginine Deiminase 2 (1 mM Ca2+) · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y2J8 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-2 (Q9Y2J8) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9Y2J8
Elsewhere: RCSB PDB 4N28 · PDBe 4N28 · UniProt Q9Y2J8

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