Research workbench
CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POPC nanodisc at 2.42 Angstrom resolution
Analyse CryoEM structure of Methylocystis sp. str. Rockwell pMMO in a POPC nanodisc at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S4M
- Type
- protein
- Length
- 2,676 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.42
- Source
- Methylocystis sp. ATCC 49242
- Molecule
- Particulate methane monooxygenase alpha subunit; Particulate methane monooxygenase beta…
- Ligands
- HXG, D10, D12, CU
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · resolution 2.42 · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Particulate methane monooxygenase alpha subunit | protein | 388 | 21% helix, 36% strand | — |
| F, B, J | Particulate methane monooxygenase beta subunit | protein | 244 | 67% helix, 4% strand | — |
| G, C, K | Ammonia monooxygenase/methane monooxygenase, subunit C family protein | protein | 241 | 78% helix, 1% strand | — |
| D, N, H | Unidentified Helix | protein | 19 | 74% helix, 0% strand | — |
Ligands and binding sites
- HXG · 1,2-dihexanoyl-sn-glycero-3-phosphocholine · ligand · 12 copies · chains F, E, B, C, A, J, K, I, G, H, D, N
- D10 · Decane · ligand · 6 copies · chains F, G, B, C, J, K
- D12 · Dodecane · ligand · 3 copies · chains J, G, F, C, B, K
- CU · Copper (II) ion · metal · 6 copies · chains A, G, C, K, E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.76 | 0.82 | 43 | HXG |
| 2 | 605 | 0.75 | 0.82 | 45 | HXG |
| 3 | 569 | 0.75 | 0.82 | 45 | HXG |
| 4 | 765 | 0.73 | 0.78 | 62 | D12, D10 |
| 5 | 689 | 0.71 | 0.77 | 51 | HXG, D12, D10 |
Interfaces
24 interfaces between chains.
- A–B · 3937 Ų buried · 27 hydrogen bonds · protein-protein
- J–I · 3929 Ų buried · 28 hydrogen bonds · protein-protein
- F–E · 3924 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 3262 Ų buried · 41 hydrogen bonds · protein-protein
- F–G · 3254 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7S4M · Cryoem structure of methylocystis sp. str. rockwell pmmo in a popc nanodisc at 2.42… · 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
- Elsewhere: RCSB PDB 7S4M · PDBe 7S4M
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