Research workbench
Sinpyl alcohol bound monolignol 4-O-methyltransferase 5
Analyse Sinpyl alcohol bound monolignol 4-O-methyltransferase 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CVU
- Type
- protein
- Length
- 1,429 residues
- Chains
- 4
- 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
- 55B, SAH, NO3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | (ISO)EUGENOL O-methyltransferase (EC 2.1.1.146) | protein | 354 | 49% helix, 17% strand | O04385 |
| B | (ISO)EUGENOL O-methyltransferase (EC 2.1.1.146) | protein | 360 | 48% helix, 17% strand | O04385 |
| D | (ISO)EUGENOL O-methyltransferase (EC 2.1.1.146) | protein | 361 | 48% helix, 17% strand | O04385 |
Ligands and binding sites
- 55B · 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenol · ligand · 4 copies · chains A, B, C, D
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.84 | 0.95 | 51 | 55B, SAH |
| 2 | 283 | 0.83 | 0.94 | 49 | 55B, SAH |
| 3 | 317 | 0.83 | 0.93 | 50 | 55B, SAH |
| 4 | 308 | 0.83 | 0.93 | 51 | 55B, SAH |
| 5 | 414 | 0.77 | 0.86 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4554 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 4446 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 583 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 576 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 5CVU · PDBe 5CVU · UniProt O04385
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