MolNFT v1 · #13847 · protein
Analogs of reaction intermediates identify a unique substrate binding site in candida rugosa lipase
1LPN: “Analogs of reaction intermediates identify a unique substrate binding site in candida rugosa lipase”. X-ray diffraction, 3 ligands (DSC, NAG, CA), 4 pockets (best druggability 0.72). MolNFT v1 #13847 on GenesisL1: 3D structure…
- PDB
- 1LPN
- Type
- protein
- Length
- 534 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- EC
- 3.1.1.3
- UniProt
- P20261
- Ligands
- DSC, NAG, CA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase (EC 3.1.1.3) | protein | 534 | 38% helix, 16% strand | P20261 |
Ligands and binding sites
- DSC · Dodecanesulfonate ion · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.72 | 0.82 | 62 | DSC |
| 2 | 95 | 0.42 | 0.78 | 16 | empty |
| 3 | 73 | 0.36 | 0.77 | 21 | empty |
| 4 | 51 | 0.26 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 2 covalent, 2 disulfide, 2 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 1LPN · Analogs of reaction intermediates identify a unique substrate binding site in candida… · the same entry in another collection · chain A against A, TM-score 1.00
- P20261 · AlphaFold monomer V2.0 prediction for lipase 1 (P20261) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P20261
- Elsewhere: RCSB PDB 1LPN · PDBe 1LPN · UniProt P20261
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