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Structure of lipase tl from capillary grown crystal in the presence of agarose

Analyse Structure of lipase tl from capillary grown crystal in the presence of agarose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7APP
Type: protein
Length: 538 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipase
EC: 3.1.1.3
UniProt: O59952
Ligands: NAG, NA
Pockets: 6 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lipase (EC 3.1.1.3)	protein	269	33% helix, 25% strand	O59952

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
NA · Sodium ion · metal · 3 copies · chains A, B
FMT · Formic acid · additive · 15 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.48	0.79	23	empty
2	104	0.48	0.80	21	empty
3	93	0.37	0.75	24	empty
4	111	0.37	0.74	23	FMT
5	101	0.36	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 622 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7APP · Structure of Lipase TL from capillary grown crystal in the presence of agarose · the same entry in another collection · chain A against A, TM-score 1.00
O59952 · AlphaFold monomer V2.0 prediction for lipase (O59952) · 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 O59952
Elsewhere: RCSB PDB 7APP · PDBe 7APP · UniProt O59952

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