Research workbench
CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC nanodisc at 2.46 Angstrom resolution
Analyse CryoEM structure of Methylotuvimicrobium alcaliphilum 20Z pMMO in a POPC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S4L
- Type
- protein
- Length
- 2,556 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.46
- Source
- Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 /…
- Molecule
- Particulate methane monooxygenase, B subunit; Particulate methane monooxygenase, A…
- EC
- 1.14.13.25
- UniProt
- G4SZ64, G4SZ63, G4SZ62
- Ligands
- HXG, D10, 6ER, CU
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · resolution 2.46 · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Particulate methane monooxygenase, B subunit (EC 1.14.13.25) | protein | 382 | 22% helix, 39% strand | G4SZ64 |
| B, F, G | Particulate methane monooxygenase, A subunit (EC 1.14.13.25) | protein | 239 | 65% helix, 5% strand | G4SZ63 |
| C, H, I | Particulate methane monooxygenase, C subunit (EC 1.14.13.25) | protein | 231 | 61% helix, 0% strand | G4SZ62 |
Ligands and binding sites
- HXG · 1,2-dihexanoyl-sn-glycero-3-phosphocholine · ligand · 15 copies · chains A, B, C, G, H, I, F, D, E
- D10 · Decane · ligand · 9 copies · chains B, C, H, I, F, G
- 6ER · (S)-2,3-bis(hexanoyloxy)propyl(2-(trimethylammonio) ethyl)phosphate · ligand · 3 copies · chains B, C, H, I, G, F
- CU · Copper (II) ion · metal · 9 copies · chains A, C, H, I, D, E
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 | 985 | 0.72 | 0.75 | 88 | empty |
| 2 | 74 | 0.72 | 0.97 | 24 | empty |
| 3 | 55 | 0.69 | 0.97 | 25 | empty |
| 4 | 67 | 0.69 | 0.96 | 19 | empty |
| 5 | 68 | 0.69 | 0.96 | 23 | empty |
Interfaces
18 interfaces between chains.
- F–D · 4051 Ų buried · 41 hydrogen bonds · protein-protein
- G–E · 4042 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4039 Ų buried · 42 hydrogen bonds · protein-protein
- H–F · 3344 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 3330 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7S4L · Cryoem structure of methylotuvimicrobium alcaliphilum 20Z pmmo in a popc nanodisc at 2.46… · 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 G4SZ64
- Every structure of UniProt G4SZ63
- Every structure of UniProt G4SZ62
- Elsewhere: RCSB PDB 7S4L · PDBe 7S4L · UniProt G4SZ64 · UniProt G4SZ63 · UniProt G4SZ62
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