Research workbench
Crystal structure of COTB2 (GGSPP/MG2+-bound form) from streptomyces melanosporofaciens
Analyse Crystal structure of COTB2 (GGSPP/MG2+-bound form) from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GUE
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- 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
- GGS, MG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyclooctat-9-en-7-ol synthase (EC 4.2.3.146) | protein | 285 | 80% helix, 0% strand | C9K1X5 |
Ligands and binding sites
- GGS · Phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6, 10,14-tetraenyl]sulfanyl-phosphinic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.79 | 0.88 | 38 | GGS |
| 2 | 440 | 0.79 | 0.87 | 40 | GGS |
| 3 | 434 | 0.79 | 0.87 | 43 | GGS |
| 4 | 410 | 0.78 | 0.87 | 39 | GGS |
| 5 | 87 | 0.73 | 0.96 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1627 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1611 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 988 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5GUE · Crystal structure of CotB2 (GGSPP/Mg2+-Bound Form) from Streptomyces melanosporofaciens · the same entry in another collection · chain D against D, 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 5GUE · PDBe 5GUE · UniProt C9K1X5
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