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Crystal structure analysis of caffeic ACID/5-hydroxyferulic acid 3/5-O-methyltransferase ferulic acid complex
Analyse Crystal structure analysis of caffeic ACID/5-hydroxyferulic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KYZ
- Type
- protein
- Length
- 1,067 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
- FER, SAH
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 47% 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, 16% strand | P28002 |
| C | Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) | protein | 356 | 46% helix, 16% strand | P28002 |
| E | Caffeic acid 3-O-methyltransferase (EC 2.1.1.68) | protein | 361 | 47% helix, 16% strand | P28002 |
Ligands and binding sites
- FER · 3-(4-hydroxy-3-methoxyphenyl)-2-propenoic acid · ligand · 3 copies · chains A, C, E
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.79 | 0.82 | 74 | SAH, FER |
| 2 | 896 | 0.79 | 0.81 | 85 | FER, SAH |
| 3 | 1073 | 0.78 | 0.80 | 81 | FER, SAH |
| 4 | 364 | 0.59 | 0.76 | 42 | empty |
| 5 | 335 | 0.57 | 0.76 | 44 | empty |
Interfaces
2 interfaces between chains.
- A–E · 4502 Ų buried · 44 hydrogen bonds · protein-protein
- C–E · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1KYZ · 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 0.95
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 1KYZ · PDBe 1KYZ · UniProt P28002
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