Research workbench
Xfel structure of the soluble methane monooxygenase hydroxylase and regulatory subunit complex, from methylosinus trichosporium OB3B, T=0 diferrous state prior to oxygen activation
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
- 6YY3
- 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
- A0A1A6FJQ4, P27353, A0A1A6FHH2, P27356
- Ligands
- FE2
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Methane monooxygenase | protein | 390 | 66% helix, 1% strand | A0A1A6FJQ4 |
| D | Methane monooxygenase component a alpha chain (EC 1.14.13.25) | protein | 515 | 62% helix, 4% strand | P27353 |
| F | Methane monooxygenase | protein | 168 | 63% helix, 4% strand | A0A1A6FHH2 |
| G | Methane monooxygenase regulatory protein B | protein | 136 | 35% helix, 29% strand | P27356 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.81 | 0.98 | 33 | empty |
| 2 | 112 | 0.79 | 0.98 | 24 | empty |
| 3 | 59 | 0.71 | 0.97 | 15 | empty |
| 4 | 229 | 0.52 | 0.76 | 28 | empty |
| 5 | 102 | 0.49 | 0.81 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 5373 Ų buried · 91 hydrogen bonds · protein-protein
- D–G · 2959 Ų buried · 46 hydrogen bonds · protein-protein
- D–F · 2232 Ų buried · 38 hydrogen bonds · protein-protein
- B–F · 1396 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 310 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6YY3 · 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 A0A1A6FJQ4
- Every structure of UniProt P27353
- Every structure of UniProt A0A1A6FHH2
- Every structure of UniProt P27356
- Elsewhere: RCSB PDB 6YY3 · PDBe 6YY3 · UniProt A0A1A6FJQ4 · UniProt P27353 · UniProt A0A1A6FHH2 · UniProt P27356
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