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A new alginate lyase (PL6) from vibrio splendidus OU02

Analyse A new alginate lyase (PL6) from vibrio splendidus OU02 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ITG
Type: protein
Length: 998 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alginate lyase
UniProt: A0A2S7V3I3
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alginate lyase	protein	499	8% helix, 36% strand	A0A2S7V3I3

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, B
MLI · Malonate ion · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	823	0.72	0.78	92	empty
2	288	0.62	0.80	39	GOL, MLI
3	290	0.61	0.79	39	MLI
4	102	0.51	0.82	19	GOL
5	98	0.48	0.81	19	GOL

Interfaces

1 interface between chains.

A–B · 624 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6ITG · a new alginate lyase (PL6) from Vibrio splendidus OU02 · 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 A0A2S7V3I3
Elsewhere: RCSB PDB 6ITG · PDBe 6ITG · UniProt A0A2S7V3I3

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