MolNFT v1 · #27823 · protein
Soluble methane monooxygenase hydroxylase: 6-bromohexanol soaked structure
1XVB · Methane monooxygenase component a alpha chain: “Soluble methane monooxygenase hydroxylase: 6-bromohexanol soaked structure”. X-ray diffraction, 6 ligands (BHL, 3BR, BBU), 20 pockets (best druggability 0.79). MolNFT v1 #27823 on…
- PDB
- 1XVB
- 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, P11987
- Ligands
- BHL, 3BR, BBU, BBX, FE, CA
- Pockets
- 20 · best druggability 0.79
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 | 62% helix, 5% strand | P22869 |
| C, D | Methane monooxygenase component a beta chain (EC 1.14.13.25) | protein | 388 | 65% helix, 1% strand | — |
| E | Methane monooxygenase component a gamma chain (EC 1.14.13.25) | protein | 166 | 64% helix, 5% strand | P11987 |
| F | Methane monooxygenase component a gamma chain (EC 1.14.13.25) | protein | 166 | 62% helix, 5% strand | P11987 |
Ligands and binding sites
- BHL · 6-bromohexan-1-ol · ligand · 10 copies · chains A, B, D
- 3BR · 1-bromopropane · ligand · 2 copies · chains B, C, D, A
- BBU · 1-bromobutane · ligand · chains A, C
- BBX · 1-bromoethane · ligand · chains B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · chains 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.79 | 0.98 | 31 | BHL |
| 2 | 135 | 0.78 | 0.96 | 26 | empty |
| 3 | 137 | 0.78 | 0.95 | 29 | empty |
| 4 | 84 | 0.77 | 0.98 | 17 | BHL |
| 5 | 70 | 0.76 | 0.99 | 20 | BHL |
Interfaces
10 interfaces between chains.
- B–D · 5241 Ų buried · 84 hydrogen bonds · protein-protein
- A–C · 5226 Ų buried · 81 hydrogen bonds · protein-protein
- A–E · 2268 Ų buried · 45 hydrogen bonds · protein-protein
- B–F · 2240 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2028 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 1XVB · soluble methane monooxygenase hydroxylase: 6-bromohexanol soaked structure · the same entry in another collection · chain F against F, 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 P11987
- Elsewhere: RCSB PDB 1XVB · PDBe 1XVB · UniProt P22869 · UniProt P11987
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