Research workbench
Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane
Analyse Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MMO
- Type
- protein
- Length
- 2,116 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methane monooxygenase hydrolase (beta chain); Methane monooxygenase hydrolase (alpha…
- EC
- 1.14.13.25
- UniProt
- P18798, P22869, P11987
- Ligands
- FE
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Methane monooxygenase hydrolase (beta chain) (EC 1.14.13.25) | protein | 384 | 65% helix, 1% strand | P18798 |
| D, E | Methane monooxygenase hydrolase (alpha chain) (EC 1.14.13.25) | protein | 512 | 63% helix, 4% strand | P22869 |
| G, H | Methane monooxygenase hydrolase (gamma chain) (EC 1.14.13.25) | protein | 162 | 65% helix, 2% strand | P11987 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains D, E
- ACY · Acetic acid · additive · 2 copies · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.80 | 0.99 | 33 | empty |
| 2 | 150 | 0.79 | 0.96 | 29 | empty |
| 3 | 856 | 0.76 | 0.80 | 92 | empty |
| 4 | 67 | 0.76 | 0.99 | 20 | empty |
| 5 | 77 | 0.75 | 0.98 | 23 | empty |
Interfaces
10 interfaces between chains.
- B–D · 5340 Ų buried · 84 hydrogen bonds · protein-protein
- C–E · 5278 Ų buried · 80 hydrogen bonds · protein-protein
- D–G · 2165 Ų buried · 38 hydrogen bonds · protein-protein
- E–H · 2123 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1845 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 1MMO · Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological… · the same entry in another collection · chain H against H, 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 B 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 G 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 D 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 P18798
- Every structure of UniProt P22869
- Every structure of UniProt P11987
- Elsewhere: RCSB PDB 1MMO · PDBe 1MMO · UniProt P18798 · UniProt P22869 · UniProt P11987
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