MolNFT v1 · #173124 · protein

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

7APP: “Structure of lipase tl from capillary grown crystal in the presence of agarose”. X-ray diffraction, 2 ligands (NAG, NA), 6 pockets (best druggability 0.48). MolNFT v1 #173124 on GenesisL1: 3D structure, binding sites and pockets in…

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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