MolNFT v1 · #167422 · protein
Crystal structure of methylosinus trichosporium OB3B soluble methane monooxygenase hydroxylase and regulatory component complex with small organic carboxylate at active center
6VK8 · Methane monooxygenase component a alpha chain: “Crystal structure of methylosinus trichosporium OB3B soluble methane monooxygenase hydroxylase and regulatory…”. X-ray diffraction, 2 ligands (BEZ, FE), 20 pockets (best druggability…
- PDB
- 6VK8
- Type
- protein
- Length
- 2,419 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methane monooxygenase component a alpha chain; Methane monooxygenase; Methane…
- UniProt
- A0A2D2D5X0, A0A2D2D5X7, A0A2D2D0T0, A0A2D2D0T8
- Ligands
- BEZ, FE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Methane monooxygenase component a alpha chain | protein | 515 | 62% helix, 4% strand | A0A2D2D5X0 |
| B, F | Methane monooxygenase | protein | 392 | 65% helix, 1% strand | A0A2D2D5X7 |
| C, G | Methane monooxygenase | protein | 168 | 63% helix, 4% strand | A0A2D2D0T0 |
| D | Methane monooxygenase regulatory protein B | protein | 132 | 39% helix, 30% strand | A0A2D2D0T8 |
| H | Methane monooxygenase regulatory protein B | protein | 137 | 37% helix, 28% strand | A0A2D2D0T8 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains E
- FE · Fe (III) ion · metal · 4 copies · chains A, E
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, C, B, H, D, E, F, G
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.86 | 0.89 | 75 | EDO |
| 2 | 144 | 0.82 | 0.98 | 33 | EDO |
| 3 | 138 | 0.81 | 0.98 | 31 | empty |
| 4 | 96 | 0.78 | 0.99 | 23 | empty |
| 5 | 96 | 0.78 | 0.98 | 25 | empty |
Interfaces
18 interfaces between chains.
- E–F · 5350 Ų buried · 94 hydrogen bonds · protein-protein
- A–B · 5343 Ų buried · 92 hydrogen bonds · protein-protein
- E–H · 2717 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2695 Ų buried · 39 hydrogen bonds · protein-protein
- E–G · 2203 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6VK8 · Crystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase… · 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 A0A2D2D5X0
- Every structure of UniProt A0A2D2D5X7
- Every structure of UniProt A0A2D2D0T0
- Every structure of UniProt A0A2D2D0T8
- Elsewhere: RCSB PDB 6VK8 · PDBe 6VK8 · UniProt A0A2D2D5X0 · UniProt A0A2D2D5X7 · UniProt A0A2D2D0T0 · UniProt A0A2D2D0T8
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