Research workbench

C. jejuni agmatine deiminase

Analyse C. jejuni agmatine deiminase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B10
Type: protein
Length: 646 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative peptidyl-arginine deiminase family protein
UniProt: Q0P9V0
Ligands: K, PO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative peptidyl-arginine deiminase family protein	protein	317	31% helix, 30% strand	Q0P9V0
B	Putative peptidyl-arginine deiminase family protein	protein	329	31% helix, 29% strand	Q0P9V0

Ligands and binding sites

K · Potassium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.77	0.98	19	empty
2	74	0.75	0.98	18	empty
3	605	0.65	0.76	67	empty
4	99	0.42	0.78	18	empty
5	90	0.38	0.77	22	empty

Interfaces

1 interface between chains.

A–B · 114 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6B10 · C. Jejuni Agmatine Deiminase · the same entry in another collection · chain A against A, TM-score 1.00

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 Q0P9V0
Elsewhere: RCSB PDB 6B10 · PDBe 6B10 · UniProt Q0P9V0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.