Research workbench
Coniferyl alcohol bound monolignol 4-O-methyltransferase 9
Analyse Coniferyl alcohol bound monolignol 4-O-methyltransferase 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CVV
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (ISO)EUGENOL O-methyltransferase
- EC
- 2.1.1.146
- UniProt
- O04385
- Ligands
- SAH, N7I
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (ISO)EUGENOL O-methyltransferase (EC 2.1.1.146) | protein | 353 | 49% helix, 16% strand | O04385 |
| B | (ISO)EUGENOL O-methyltransferase (EC 2.1.1.146) | protein | 347 | 50% helix, 16% strand | O04385 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- N7I · 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.82 | 0.93 | 45 | SAH |
| 2 | 274 | 0.81 | 0.92 | 45 | SAH, N7I |
| 3 | 62 | 0.70 | 0.96 | 26 | empty |
| 4 | 200 | 0.58 | 0.80 | 20 | empty |
| 5 | 179 | 0.48 | 0.76 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 4492 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5CVV · coniferyl alcohol bound monolignol 4-O-methyltransferase 9 · the same entry in another collection · chain B against B, TM-score 1.00
- O04385 · AlphaFold monomer V2.0 prediction for (ISO)EUGENOL O-methyltransferase (O04385) · 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 O04385
- Elsewhere: RCSB PDB 5CVV · PDBe 5CVV · UniProt O04385
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