Research workbench
Crystal structure of reduced methylosinus trichosporium OB3B soluble methane monooxygenase hydroxylase
Analyse Crystal structure of reduced 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
- 6VK7
- Type
- protein
- Length
- 1,070 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methane monooxygenase component a alpha chain; Methane monooxygenase
- UniProt
- A0A2D2D5X0, A0A2D2D5X7, A0A2D2D0T0
- Ligands
- FE
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methane monooxygenase component a alpha chain | protein | 515 | 61% helix, 4% strand | A0A2D2D5X0 |
| B | Methane monooxygenase | protein | 387 | 67% helix, 1% strand | A0A2D2D5X7 |
| C | Methane monooxygenase | protein | 168 | 63% helix, 4% strand | A0A2D2D0T0 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.78 | 0.99 | 31 | empty |
| 2 | 94 | 0.77 | 0.98 | 23 | empty |
| 3 | 66 | 0.73 | 0.98 | 18 | empty |
| 4 | 121 | 0.51 | 0.81 | 22 | empty |
| 5 | 137 | 0.49 | 0.79 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5350 Ų buried · 90 hydrogen bonds · protein-protein
- A–C · 2200 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1408 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6VK7 · Crystal Structure of reduced Methylosinus trichosporium OB3b Soluble Methane… · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 6VK7 · PDBe 6VK7 · UniProt A0A2D2D5X0 · UniProt A0A2D2D5X7 · UniProt A0A2D2D0T0
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