Research workbench
Crystal structure of methylosinus trichosporium OB3B soluble methane monooxygenase hydroxylase and regulatory component complex with small organic carboxylate at active center
Analyse Crystal structure of methylosinus trichosporium OB3B soluble methane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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