Research workbench
Crystal structure of the quaternary ammonium rieske monooxygenase cnta in complex with substrate L-carnitine
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
- 6Y9D
- Type
- protein
- Length
- 4,224 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, 152, FE, SCN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Carnitine monooxygenase oxygenase subunit (EC 1.14.13.239) | protein | 352 | 29% helix, 28% 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
- 152 · Carnitine · 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
- SCN · Thiocyanate ion · ion · 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, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.79 | 0.87 | 48 | FE, 152, SCN |
| 2 | 370 | 0.77 | 0.86 | 44 | 152, SCN |
| 3 | 356 | 0.77 | 0.87 | 47 | 152, SCN |
| 4 | 830 | 0.76 | 0.79 | 83 | 152, SCN |
| 5 | 411 | 0.75 | 0.84 | 45 | FE, 152, SCN |
Interfaces
18 interfaces between chains.
- B–C · 1436 Ų buried · 32 hydrogen bonds · protein-protein
- K–L · 1431 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1429 Ų buried · 32 hydrogen bonds · protein-protein
- H–I · 1413 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1413 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6Y9D · 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 6Y9D · PDBe 6Y9D · UniProt A0A059ZPP5
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