Research workbench
Crystal structure of COTB2 variant W288F in complex with alendronate
Analyse Crystal structure of COTB2 variant W288F in complex with alendronate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AO1
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclooctat-9-en-7-ol synthase
- EC
- 4.2.3.146
- UniProt
- C9K1X5
- Ligands
- AHD, MG, CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclooctat-9-en-7-ol synthase (EC 4.2.3.146) | protein | 302 | 73% helix, 1% strand | C9K1X5 |
| B | Cyclooctat-9-en-7-ol synthase (EC 4.2.3.146) | protein | 296 | 75% helix, 1% strand | C9K1X5 |
Ligands and binding sites
- AHD · 4-amino-1-hydroxybutane-1,1-diyldiphosphonate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.82 | 0.93 | 42 | AHD, MG, CL, MPD |
| 2 | 268 | 0.80 | 0.92 | 37 | AHD, MG, CL, MPD |
| 3 | 162 | 0.79 | 0.95 | 16 | MPD |
| 4 | 260 | 0.66 | 0.83 | 36 | empty |
| 5 | 58 | 0.43 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1490 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7AO1 · Crystal structure of CotB2 variant W288F in complex with alendronate · 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 B 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 7AO1 · PDBe 7AO1 · UniProt C9K1X5
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