Research workbench
Crystal structure of apo methane monooxygenase hydroxylase from M. capsulatus (bath)
Analyse Crystal structure of apo methane monooxygenase hydroxylase from M. capsulatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XMG
- Type
- protein
- Length
- 2,128 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methane monooxygenase component a alpha chain; Methane monooxygenase component a beta…
- EC
- 1.14.13.25
- UniProt
- P22869, P18798, P11987
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methane monooxygenase component a alpha chain (EC 1.14.13.25) | protein | 510 | 61% helix, 5% strand | P22869 |
| C, D | Methane monooxygenase component a beta chain (EC 1.14.13.25) | protein | 388 | 65% helix, 1% strand | P18798 |
| E | Methane monooxygenase component a gamma chain (EC 1.14.13.25) | protein | 166 | 64% helix, 6% strand | P11987 |
| F | Methane monooxygenase component a gamma chain (EC 1.14.13.25) | protein | 166 | 63% helix, 5% strand | P11987 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.78 | 0.97 | 26 | empty |
| 2 | 709 | 0.75 | 0.80 | 80 | empty |
| 3 | 63 | 0.74 | 0.99 | 23 | empty |
| 4 | 63 | 0.73 | 0.98 | 23 | empty |
| 5 | 69 | 0.72 | 0.97 | 21 | empty |
Interfaces
10 interfaces between chains.
- B–D · 5252 Ų buried · 88 hydrogen bonds · protein-protein
- A–C · 5224 Ų buried · 88 hydrogen bonds · protein-protein
- A–E · 2249 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 2249 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2049 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 1XMG · Crystal structure of apo methane monooxygenase hydroxylase from M. capsulatus (Bath) · the same entry in another collection · chain F against F, TM-score 1.00
- P18798 · AlphaFold monomer V2.0 prediction for methane monooxygenase component a beta chain… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P22869 · AlphaFold monomer V2.0 prediction for methane monooxygenase component a alpha chain… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P11987 · AlphaFold monomer V2.0 prediction for methane monooxygenase component a gamma chain… · a predicted model of the same protein · chain E 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 P22869
- Every structure of UniProt P18798
- Every structure of UniProt P11987
- Elsewhere: RCSB PDB 1XMG · PDBe 1XMG · UniProt P22869 · UniProt P18798 · UniProt P11987
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