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Crystal structure of alginate lyase val-1 from chlorella virus

Analyse Crystal structure of alginate lyase val-1 from chlorella virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GNE
Type: protein
Length: 485 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Val-1
EC: 4.2.2.3
UniProt: Q9DTZ2
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Val-1 (EC 4.2.2.3)	protein	243	4% helix, 48% strand	Q9DTZ2
B	Val-1 (EC 4.2.2.3)	protein	242	4% helix, 48% strand	Q9DTZ2

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains A, B
FLC · Citrate anion · additive · 2 copies · chains A, B

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	928	0.76	0.79	88	FLC, GOL
2	102	0.44	0.78	23	empty

Interfaces

1 interface between chains.

A–B · 588 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3GNE · Crystal structure of alginate lyase vAL-1 from Chlorella virus · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q9DTZ2
Elsewhere: RCSB PDB 3GNE · PDBe 3GNE · UniProt Q9DTZ2

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