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Crystal structure of the quaternary ammonium rieske monooxygenase cnta in complex with inhibitor MMV12 (MMV020670)
Analyse Crystal structure of the quaternary ammonium rieske monooxygenase cnta in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZGP
- Type
- protein
- Length
- 4,305 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carnitine monooxygenase oxygenase subunit
- EC
- 1.14.13.239
- UniProt
- A0A059ZPP5
- Ligands
- FES, QKQ, FE
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 360 | 26% helix, 30% strand | A0A059ZPP5 |
| B | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 357 | 27% helix, 29% strand | A0A059ZPP5 |
| C | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 357 | 27% helix, 29% strand | A0A059ZPP5 |
| F | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 359 | 26% helix, 29% strand | A0A059ZPP5 |
| G | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 363 | 25% helix, 28% strand | A0A059ZPP5 |
| H, L | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 358 | 26% helix, 32% strand | A0A059ZPP5 |
| I | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 358 | 27% helix, 29% strand | A0A059ZPP5 |
| J | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 356 | 26% helix, 29% strand | A0A059ZPP5 |
| K | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 359 | 26% helix, 30% strand | A0A059ZPP5 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- QKQ · ~{N}-(3-imidazol-1-ylpropyl)-8-(4-methoxyphenyl)-1,6-naphthyridine-2-carboxamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.83 | 0.97 | 33 | QKQ |
| 2 | 321 | 0.80 | 0.90 | 45 | FE, QKQ |
| 3 | 351 | 0.80 | 0.89 | 47 | QKQ |
| 4 | 291 | 0.79 | 0.90 | 36 | FE, QKQ |
| 5 | 263 | 0.78 | 0.90 | 37 | FE, QKQ |
Interfaces
21 interfaces between chains.
- K–L · 1427 Ų buried · 35 hydrogen bonds · protein-protein
- J–L · 1426 Ų buried · 33 hydrogen bonds · protein-protein
- J–K · 1426 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1418 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1413 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6ZGP · Crystal structure of the quaternary ammonium Rieske monooxygenase CntA in complex with… · 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 A0A059ZPP5
- Elsewhere: RCSB PDB 6ZGP · PDBe 6ZGP · UniProt A0A059ZPP5
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