MolNFT v1 · #129819 · protein
Thiobacillus denitrificans bph in complex with epoxomicin
5OVT: “Thiobacillus denitrificans bph in complex with epoxomicin”. X-ray diffraction, 3 ligands (ACE, 6VO, PO4), 10 pockets (best druggability 0.37). MolNFT v1 #129819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OVT
- Type
- protein
- Length
- 1,302 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bph; Epoxomicin
- Ligands
- ACE, 6VO, PO4
- Pockets
- 10 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Bph | protein | 183 | 30% helix, 32% strand | — |
| a, b, c, d, e, f, g | Epoxomicin | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 7 copies · chains A, G, a, B, b, C, c, D, d, E, e, F, f, g
- 6VO · (3~{R},4~{S})-4-azanyl-2,6-dimethyl-heptane-2,3-diol · ligand · 7 copies · chains A, a, B, b, C, c, D, d, E, e, F, f, G, g
- PO4 · Phosphate ion · ion · 7 copies · chains A, a, C, c, E, e, G, g, B, b, D, d, F, f
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.37 | 0.74 | 25 | PO4 |
| 2 | 98 | 0.35 | 0.74 | 19 | 6VO, PO4 |
| 3 | 83 | 0.34 | 0.75 | 18 | 6VO, PO4 |
| 4 | 101 | 0.33 | 0.73 | 19 | 6VO, PO4 |
| 5 | 95 | 0.33 | 0.73 | 20 | 6VO, PO4 |
Interfaces
21 interfaces between chains.
- C–D · 1145 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1141 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1138 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 1138 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1136 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 modified, 21 covalent (engineered, covalent ligand, nonstandard).
Compared structures
- 5OVT · Thiobacillus denitrificans BPH in complex with Epoxomicin · 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
- Elsewhere: RCSB PDB 5OVT · PDBe 5OVT
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