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Structure of lipase B from lasiodiplodia theobromae

Analyse Structure of lipase B from lasiodiplodia theobromae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7V6D
Type: protein
Length: 733 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipase B
UniProt: A0A5N5DNA6
Ligands: NAG, CA
Pockets: 2 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipase B	protein	367	39% helix, 11% strand	A0A5N5DNA6
B	Lipase B	protein	366	39% helix, 11% strand	A0A5N5DNA6

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
CA · Calcium ion · metal · 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	1187	0.87	0.88	108	empty
2	101	0.40	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 1222 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7V6D · Structure of lipase B from Lasiodiplodia theobromae · 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 A0A5N5DNA6
Elsewhere: RCSB PDB 7V6D · PDBe 7V6D · UniProt A0A5N5DNA6

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