Research workbench
Crystal structure of a putative lipase from bacteroides thetaiotaomicron
Analyse Crystal structure of a putative lipase from bacteroides thetaiotaomicron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BZW
- Type
- protein
- Length
- 1,479 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative lipase
- UniProt
- Q8A3J3
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative lipase | protein | 248 | 36% helix, 23% strand | Q8A3J3 |
| B, C, D, E | Putative lipase | protein | 247 | 36% helix, 23% strand | Q8A3J3 |
| F | Putative lipase | protein | 243 | 36% helix, 24% strand | Q8A3J3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, F, A, D
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.82 | 0.84 | 50 | empty |
| 2 | 876 | 0.82 | 0.84 | 52 | empty |
| 3 | 812 | 0.76 | 0.80 | 104 | SO4 |
| 4 | 359 | 0.68 | 0.81 | 45 | SO4 |
| 5 | 89 | 0.55 | 0.86 | 20 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1802 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1796 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1778 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1776 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1775 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3BZW · Crystal structure of a putative lipase from Bacteroides thetaiotaomicron · 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 Q8A3J3
- Elsewhere: RCSB PDB 3BZW · PDBe 3BZW · UniProt Q8A3J3
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