MolNFT v1 · #113594 · protein

Structure of C351A mutant of porphyromonas gingivalis peptidylarginine deiminase

5AK8: “Structure of C351A mutant of porphyromonas gingivalis peptidylarginine deiminase”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.74). MolNFT v1 #113594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AK8
Type: protein
Length: 421 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidylarginine deiminase
EC: 3.5.3.-
UniProt: Q9RQJ2
Ligands: NA
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidylarginine deiminase (EC 3.5.3.-)	protein	421	22% helix, 36% strand	Q9RQJ2

Ligands and binding sites

NA · Sodium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 18 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.74	0.99	27	EDO
2	133	0.70	0.90	37	EDO
3	106	0.41	0.76	20	EDO

Compared structures

5AK8 · Structure of C351A mutant of Porphyromonas gingivalis peptidylarginine deiminase · the same entry in another collection · chain A against A, TM-score 1.00
Q9RQJ2 · AlphaFold monomer V2.0 prediction for peptidylarginine deiminase (Q9RQJ2) · 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 Q9RQJ2
Elsewhere: RCSB PDB 5AK8 · PDBe 5AK8 · UniProt Q9RQJ2

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