Research workbench
Xfel structure of the soluble methane monooxygenase hydroxylase and regulatory subunit complex, from methylosinus trichosporium OB3B, diferric state
Analyse Xfel structure of the soluble methane monooxygenase hydroxylase and regulatory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YD0
- Type
- protein
- Length
- 1,209 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methane monooxygenase; Methane monooxygenase component a alpha chain; Methane…
- EC
- 1.14.13.25
- UniProt
- A0A2D2D5X7, P27353, A0A1A6FHH2, P27356
- Ligands
- FE
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Methane monooxygenase | protein | 390 | 67% helix, 1% strand | A0A2D2D5X7 |
| D | Methane monooxygenase component a alpha chain (EC 1.14.13.25) | protein | 515 | 63% helix, 4% strand | P27353 |
| F | Methane monooxygenase | protein | 168 | 63% helix, 4% strand | A0A1A6FHH2 |
| G | Methane monooxygenase regulatory protein B | protein | 136 | 36% helix, 29% strand | P27356 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.80 | 0.97 | 31 | empty |
| 2 | 106 | 0.78 | 0.98 | 25 | empty |
| 3 | 67 | 0.71 | 0.97 | 19 | empty |
| 4 | 213 | 0.53 | 0.78 | 27 | empty |
| 5 | 185 | 0.50 | 0.77 | 21 | empty |
Interfaces
5 interfaces between chains.
- B–D · 5464 Ų buried · 91 hydrogen bonds · protein-protein
- D–G · 2962 Ų buried · 47 hydrogen bonds · protein-protein
- D–F · 2225 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 1401 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 304 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6YD0 · XFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit… · the same entry in another collection · chain B against B, TM-score 1.00
- P27353 · AlphaFold monomer V2.0 prediction for methane monooxygenase component a alpha chain… · a predicted model of the same protein · chain D against A, TM-score 0.98
- P27356 · AlphaFold monomer V2.0 prediction for methane monooxygenase regulatory protein B (P27356) · a predicted model of the same protein · chain G against A, TM-score 0.93
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 A0A2D2D5X7
- Every structure of UniProt P27353
- Every structure of UniProt A0A1A6FHH2
- Every structure of UniProt P27356
- Elsewhere: RCSB PDB 6YD0 · PDBe 6YD0 · UniProt A0A2D2D5X7 · UniProt P27353 · UniProt A0A1A6FHH2 · UniProt P27356
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