MolNFT v1 · #167420 · protein
Crystal structure of methylosinus trichosporium OB3B soluble methane monooxygenase hydroxylase
6VK6 · Methane monooxygenase component a alpha chain: “Crystal structure of methylosinus trichosporium OB3B soluble methane monooxygenase hydroxylase”. X-ray diffraction, 2 ligands (FE, CL), 9 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6VK6
- 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, CL
- Pockets
- 9 · best druggability 0.82
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
- CL · Chloride ion · ion · 4 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 42 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.82 | 0.98 | 35 | EDO |
| 2 | 110 | 0.78 | 0.98 | 25 | empty |
| 3 | 112 | 0.68 | 0.90 | 26 | EDO |
| 4 | 170 | 0.58 | 0.82 | 31 | EDO |
| 5 | 206 | 0.52 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5361 Ų buried · 89 hydrogen bonds · protein-protein
- A–C · 2218 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1399 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6VK6 · 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
- Elsewhere: RCSB PDB 6VK6 · PDBe 6VK6 · UniProt A0A2D2D5X0 · UniProt A0A2D2D5X7 · UniProt A0A2D2D0T0
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