Research workbench
Crystal structure of particulate methane monooxygenase from methylococcus capsulatus (bath)
Analyse Crystal structure of particulate methane monooxygenase from methylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RGB
- Type
- protein
- Length
- 2,439 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methane monooxygenase subunit B2; Methane monooxygenase subunit A2; Methane monooxygenase…
- EC
- 1.14.13.25
- UniProt
- Q49104, Q607G3, O05111
- Ligands
- CUA, ZN, CU
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Methane monooxygenase subunit B2 (EC 1.14.13.25) | protein | 382 | 19% helix, 38% strand | Q49104 |
| B, J, F | Methane monooxygenase subunit A2 (EC 1.14.13.25) | protein | 218 | 72% helix, 4% strand | Q607G3 |
| C, K, G | Methane monooxygenase subunit C2 (EC 1.14.13.25) | protein | 213 | 68% helix, 0% strand | O05111 |
Ligands and binding sites
- CUA · Dinuclear copper ion · ligand · 3 copies · chains A, E, I
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, E, I, J, K, F, G
- CU · Copper (II) ion · metal · 3 copies · chains A, 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 | 924 | 0.77 | 0.79 | 86 | ZN |
| 2 | 854 | 0.75 | 0.78 | 84 | empty |
| 3 | 563 | 0.71 | 0.80 | 57 | empty |
| 4 | 579 | 0.70 | 0.79 | 61 | empty |
| 5 | 417 | 0.69 | 0.80 | 45 | ZN |
Interfaces
18 interfaces between chains.
- I–J · 3687 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 3680 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3679 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2891 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 2888 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3RGB · Crystal structure of particulate methane monooxygenase from Methylococcus capsulatus… · the same entry in another collection · chain G against G, 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 0.98
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 Q49104
- Every structure of UniProt Q607G3
- Every structure of UniProt O05111
- Elsewhere: RCSB PDB 3RGB · PDBe 3RGB · UniProt Q49104 · UniProt Q607G3 · UniProt O05111
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