MolNFT v1 · #170631 · protein
Xfel structure of the soluble methane monooxygenase hydroxylase and regulatory subunit complex, from methylosinus trichosporium OB3B, diferrous state
6YDI: “Xfel structure of the soluble methane monooxygenase hydroxylase and regulatory subunit complex, from…”. X-ray diffraction, 1 ligand (FE2), 14 pockets (best druggability 0.80). MolNFT v1 #170631 on GenesisL1: 3D structure, binding…
- PDB
- 6YDI
- Type
- protein
- Length
- 1,204 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
- FE2
- Pockets
- 14 · 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 | 389 | 66% helix, 1% strand | A0A2D2D5X7 |
| D | Methane monooxygenase component a alpha chain (EC 1.14.13.25) | protein | 511 | 63% helix, 4% strand | P27353 |
| F | Methane monooxygenase | protein | 168 | 63% helix, 4% strand | A0A1A6FHH2 |
| G | Methane monooxygenase regulatory protein B | protein | 136 | 38% helix, 29% strand | P27356 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.80 | 0.97 | 33 | empty |
| 2 | 116 | 0.79 | 0.98 | 27 | empty |
| 3 | 66 | 0.71 | 0.96 | 17 | empty |
| 4 | 168 | 0.49 | 0.77 | 19 | empty |
| 5 | 163 | 0.49 | 0.77 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–D · 5388 Ų buried · 88 hydrogen bonds · protein-protein
- D–G · 2966 Ų buried · 43 hydrogen bonds · protein-protein
- D–F · 2230 Ų buried · 33 hydrogen bonds · protein-protein
- B–F · 1384 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 308 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6YDI · 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 0.99
- 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 6YDI · PDBe 6YDI · UniProt A0A2D2D5X7 · UniProt P27353 · UniProt A0A1A6FHH2 · UniProt P27356
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