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Crystal structure of the closed state of lipase 2 from candida rugosa

Analyse Crystal structure of the closed state of lipase 2 from candida rugosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GZ7
Type: protein
Length: 2,136 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipase 2
EC: 3.1.1.3
UniProt: P32946
Ligands: NAG
Pockets: 15 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Lipase 2 (EC 3.1.1.3)	protein	534	37% helix, 15% strand	P32946

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
GOL · Glycerol · additive · 8 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.78	0.98	29	empty
2	93	0.77	0.97	27	empty
3	78	0.76	0.98	28	empty
4	79	0.74	0.97	28	empty
5	905	0.72	0.76	93	empty

Interfaces

5 interfaces between chains.

A–D · 672 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 449 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 219 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 86 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 42 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

1GZ7 · Crystal structure of the closed state of lipase 2 from Candida rugosa · the same entry in another collection · chain D against D, TM-score 1.00
P32946 · AlphaFold monomer V2.0 prediction for lipase 2 (P32946) · a predicted model of the same protein · chain A 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 P32946
Elsewhere: RCSB PDB 1GZ7 · PDBe 1GZ7 · UniProt P32946

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