MolNFT v1 · #13022 · protein
Crystal structure analysis of caffeic ACID/5-hydroxyferulic acid 3/5-O-methyltransferase in complex with 5- hydroxyconiferaldehyde
1KYW · Caffeic acid 3-O-methyltransferase: “Crystal structure analysis of caffeic ACID/5-hydroxyferulic acid 3/5-O-methyltransferase in complex with 5…”. X-ray diffraction, 2 ligands (SAH, HFL), 8 pockets (best druggability 0.79). MolNFT…
- PDB
- 1KYW
- Type
- protein
- Length
- 1,072 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caffeic acid 3-O-methyltransferase
- EC
- 2.1.1.68
- UniProt
- P28002
- Ligands
- SAH, HFL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) | protein | 350 | 47% helix, 15% strand | P28002 |
| C, F | Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) | protein | 361 | 44% helix, 16% strand | P28002 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains C, F
- HFL · 5-(3,3-dihydroxypropeny)-3-methoxy-benzene-1,2-diol · ligand · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.79 | 0.81 | 74 | SAH, HFL |
| 2 | 860 | 0.79 | 0.81 | 72 | SAH |
| 3 | 740 | 0.76 | 0.80 | 58 | empty |
| 4 | 357 | 0.59 | 0.76 | 42 | empty |
| 5 | 296 | 0.55 | 0.76 | 40 | empty |
Interfaces
2 interfaces between chains.
- A–F · 4503 Ų buried · 47 hydrogen bonds · protein-protein
- C–F · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1KYW · Crystal Structure Analysis of Caffeic Acid/5-hydroxyferulic acid 3/5-O-methyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- P28002 · AlphaFold monomer V2.0 prediction for caffeic acid 3-O-methyltransferase (P28002) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P28002
- Elsewhere: RCSB PDB 1KYW · PDBe 1KYW · UniProt P28002
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