Research workbench
Analogs of reaction intermediates identify a unique substrate binding site in candida rugosa lipase
Analyse Analogs of reaction intermediates identify a unique substrate binding site in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LPO
- 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
- HDS, NAG, CA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase (EC 3.1.1.3) | protein | 534 | 37% helix, 15% strand | P20261 |
Ligands and binding sites
- HDS · 1-hexadecanosulfonic acid · ligand · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.70 | 0.80 | 60 | HDS |
| 2 | 89 | 0.41 | 0.78 | 16 | empty |
| 3 | 59 | 0.32 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 1LPO · 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 1LPO · PDBe 1LPO · UniProt P20261
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