MolNFT v1 · #13443 · protein

Lipase (E.C.3.1.1.3) (triacylglycerol hydrolase)

1LBS · Lipase B: “Lipase (E.C.3.1.1.3) (triacylglycerol hydrolase)”. X-ray diffraction, 2 ligands (HEE, NAG), 10 pockets (best druggability 0.81). MolNFT v1 #13443 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1LBS
Type: protein
Length: 1,902 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipase B
EC: 3.1.1.3
UniProt: P41365
Ligands: HEE, NAG
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Lipase B (EC 3.1.1.3)	protein	317	39% helix, 16% strand	P41365

Ligands and binding sites

HEE · N-hexylphosphonate ethyl ester · ligand · 6 copies · chains A, B, C, D, E, F
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F

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

Pockets

10 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	942	0.81	0.83	85	HEE
2	883	0.81	0.83	99	empty
3	1191	0.79	0.81	91	HEE
4	1179	0.79	0.81	94	HEE
5	204	0.46	0.74	24	empty

Interfaces

7 interfaces between chains.

A–B · 371 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 371 Å² buried · 0 hydrogen bonds · protein-protein
E–F · 371 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 320 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 320 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 6 covalent, 6 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

1LBS · Lipase (E.C.3.1.1.3) (triacylglycerol hydrolase) · the same entry in another collection · chain C against C, TM-score 1.00
P41365 · AlphaFold monomer V2.0 prediction for lipase B (P41365) · a predicted model of the same protein · 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 P41365
Elsewhere: RCSB PDB 1LBS · PDBe 1LBS · UniProt P41365

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