Research workbench
Crystal structure of a lipase carboxylesterase from Sulfolobus islandicus
Analyse Crystal structure of a lipase carboxylesterase from Sulfolobus islandicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LK6
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Sulfolobus islandicus (strain REY15A)
- Molecule
- Alpha/beta hydrolase fold-3 domain protein
- UniProt
- F0NDQ1
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.6 · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alpha/beta hydrolase fold-3 domain protein | protein | 302 | 40% helix, 18% strand | F0NDQ1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.79 | 0.83 | 90 | empty |
| 2 | 94 | 0.75 | 0.96 | 19 | empty |
| 3 | 835 | 0.75 | 0.79 | 79 | empty |
| 4 | 97 | 0.74 | 0.95 | 20 | empty |
| 5 | 86 | 0.74 | 0.96 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1362 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1317 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 867 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 837 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 266 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5LK6 · Crystal structure of a lipase carboxylesterase from sulfolobus islandicus · the same entry in another collection · 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 F0NDQ1
- Elsewhere: RCSB PDB 5LK6 · PDBe 5LK6 · UniProt F0NDQ1
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