Research workbench
Crystal structure of the bacterial diterpene cyclase COTB2 variant F149L
Analyse Crystal structure of the bacterial diterpene cyclase COTB2 variant F149L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OMH
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl diphosphate cyclase
- UniProt
- C9K1X5
- Ligands
- NA
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl diphosphate cyclase | protein | 280 | 79% helix, 0% strand | C9K1X5 |
| B | Geranylgeranyl diphosphate cyclase | protein | 282 | 79% helix, 0% strand | C9K1X5 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.77 | 0.84 | 42 | empty |
| 2 | 579 | 0.76 | 0.83 | 48 | empty |
| 3 | 309 | 0.69 | 0.83 | 36 | empty |
| 4 | 147 | 0.64 | 0.87 | 23 | empty |
| 5 | 54 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1550 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4OMH · Crystal structure of the bacterial diterpene cyclase COTB2 variant F149L · the same entry in another collection · chain A against A, TM-score 1.00
- C9K1X5 · AlphaFold monomer V2.0 prediction for cyclooctat-9-en-7-ol synthase (C9K1X5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 C9K1X5
- Elsewhere: RCSB PDB 4OMH · PDBe 4OMH · UniProt C9K1X5
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