MolNFT v1 · #152773 · protein

Structure of candida antarctica lipase B mutant

6ISP: “Structure of candida antarctica lipase B mutant”. X-ray diffraction, 2 ligands (CPQ, CA), 5 pockets (best druggability 0.81). MolNFT v1 #152773 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ISP
Type: protein
Length: 1,270 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipase B
EC: 3.1.1.3
UniProt: P41365
Ligands: CPQ, CA
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, B	Lipase B (EC 3.1.1.3)	protein	317	36% helix, 16% strand	P41365
A	Lipase B (EC 3.1.1.3)	protein	317	36% helix, 16% strand	P41365
C	Lipase B (EC 3.1.1.3)	protein	319	35% helix, 16% strand	P41365

Ligands and binding sites

CPQ · N,N-bis(3-D-gluconamidopropyl)deoxycholamide · ligand · 11 copies · chains D, A, C, B
CA · Calcium ion · metal · 2 copies · chains D, A, C, B

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

Pockets

5 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	1169	0.81	0.82	129	CA, CPQ
2	1192	0.80	0.81	136	CPQ
3	528	0.71	0.80	54	empty
4	75	0.33	0.74	14	empty
5	55	0.32	0.76	15	empty

Interfaces

3 interfaces between chains.

A–C · 715 Å² buried · 4 hydrogen bonds · protein-protein
C–B · 602 Å² buried · 0 hydrogen bonds · protein-protein
D–A · 597 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

6ISP · structure of Candida antarctica Lipase B mutant · the same entry in another collection · chain D against D, TM-score 1.00
P41365 · AlphaFold monomer V2.0 prediction for lipase B (P41365) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 6ISP · PDBe 6ISP · UniProt P41365

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