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MolNFT v1 · #152775 · protein

Structure of lipase mutant with cys-his-asp catalytic triad

6ISR · Lipase B: “Structure of lipase mutant with cys-his-asp catalytic triad”. X-ray diffraction, 1 ligand (NI), 3 pockets (best druggability 0.61). MolNFT v1 #152775 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6ISR
Type
protein
Length
628 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Lipase B
EC
3.1.1.3
UniProt
P41365
Ligands
NI
Pockets
3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BLipase B (EC 3.1.1.3)protein31435% helix, 15% strandP41365

Ligands and binding sites

  • NI · Nickel (II) ion · metal · 2 copies · chains A, B
  • PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
  • PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12080.610.8237NI
22030.580.8137NI
32430.520.7629empty

Interfaces

1 interface between chains.

  • A–B · 123 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

  • 6ISR · structure of lipase mutant with Cys-His-Asp catalytic triad · the same entry in another collection · chain A against A, 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 0.97

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