Research workbench
Cryoem structure of methylococcus capsulatus (bath) pmmo in a native lipid nanodisc at 2.34 ångström resolution
Analyse Cryoem structure of methylococcus capsulatus (bath) pmmo in a native lipid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S4K
- Type
- protein
- Length
- 2,577 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Particulate methane monooxygenase alpha subunit; Ammonia MONOOXYGENASE/METHANE…
- EC
- 1.14.18.3, 1.14.13.25
- UniProt
- G1UBD1, Q603F1, Q607G3
- Ligands
- D10, PLC, P1O, HXG, CU
- Pockets
- 20 · best druggability 0.68
Structure
electron microscopy · 3 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Particulate methane monooxygenase alpha subunit (EC 1.14.18.3) | protein | 382 | 20% helix, 38% strand | G1UBD1 |
| C, G, K | Ammonia MONOOXYGENASE/METHANE monooxygenase, subunit C family protein (EC 1.14.13.25) | protein | 236 | 72% helix, 1% strand | Q603F1 |
| B, F, J | Particulate methane monooxygenase beta subunit (EC 1.14.18.3) | protein | 241 | 69% helix, 5% strand | Q607G3 |
Ligands and binding sites
- D10 · Decane · ligand · 18 copies · chains A, B, E, I, F, J
- PLC · Diundecyl phosphatidyl choline · ligand · 18 copies · chains C, F, A, B, I, K, G, E, J
- P1O · 1,2-didecanoyl-sn-glycero-3-phosphocholine · ligand · 12 copies · chains C, B, F, A, K, J, G, E, I
- HXG · 1,2-dihexanoyl-sn-glycero-3-phosphocholine · ligand · 6 copies · chains A, C, B, G, E, F, K, I, J
- CU · Copper (II) ion · metal · 9 copies · chains A, C, G, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.68 | 0.75 | 55 | PLC, P1O |
| 2 | 651 | 0.68 | 0.76 | 55 | PLC, P1O |
| 3 | 317 | 0.62 | 0.78 | 34 | P1O |
| 4 | 309 | 0.61 | 0.78 | 33 | P1O |
| 5 | 275 | 0.60 | 0.78 | 26 | P1O |
Interfaces
21 interfaces between chains.
- E–F · 4045 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 4035 Ų buried · 46 hydrogen bonds · protein-protein
- I–J · 4035 Ų buried · 47 hydrogen bonds · protein-protein
- C–B · 3307 Ų buried · 36 hydrogen bonds · protein-protein
- K–J · 3304 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 7S4K · CryoEM structure of Methylococcus capsulatus (Bath) pMMO in a native lipid nanodisc at… · the same entry in another collection · chain J against J, TM-score 1.00
- Q607G3 · AlphaFold monomer V2.0 prediction for particulate methane monooxygenase beta subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- G1UBD1 · AlphaFold monomer V2.0 prediction for particulate methane monooxygenase alpha subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 G1UBD1
- Every structure of UniProt Q603F1
- Every structure of UniProt Q607G3
- Elsewhere: RCSB PDB 7S4K · PDBe 7S4K · UniProt G1UBD1 · UniProt Q603F1 · UniProt Q607G3
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