Research workbench
Crystal structure of BIOH3 from mycolicibacterium smegmatis
Analyse Crystal structure of BIOH3 from mycolicibacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WWF
- Type
- protein
- Length
- 1,654 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Esterase
- UniProt
- A0A8B4QLS5
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Esterase | protein | 277 | 40% helix, 14% strand | A0A8B4QLS5 |
| B, D, E, F | Esterase | protein | 275 | 40% helix, 15% strand | A0A8B4QLS5 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.61 | 0.85 | 23 | PEG |
| 2 | 137 | 0.59 | 0.84 | 21 | PEG |
| 3 | 130 | 0.59 | 0.84 | 27 | PEG |
| 4 | 135 | 0.58 | 0.83 | 24 | PEG |
| 5 | 151 | 0.57 | 0.82 | 22 | PEG |
Interfaces
5 interfaces between chains.
- C–D · 1882 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1810 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1792 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 589 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 7WWF · Crystal structure of BioH3 from Mycolicibacterium smegmatis · 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 A0A8B4QLS5
- Elsewhere: RCSB PDB 7WWF · PDBe 7WWF · UniProt A0A8B4QLS5
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