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Crystal structure of perennial ryegrass LPOMT1 complexed with S- adenosyl-L-homocysteine and coniferaldehyde
Analyse Crystal structure of perennial ryegrass LPOMT1 complexed with S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P9K
- Type
- protein
- Length
- 1,421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caffeic acid O-methyltransferase
- EC
- 2.1.1.6
- UniProt
- Q9ZTU2
- Ligands
- SAH, CIY
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Caffeic acid O-methyltransferase (EC 2.1.1.6) | protein | 357 | 51% helix, 17% strand | Q9ZTU2 |
| B | Caffeic acid O-methyltransferase (EC 2.1.1.6) | protein | 356 | 49% helix, 17% strand | Q9ZTU2 |
| D | Caffeic acid O-methyltransferase (EC 2.1.1.6) | protein | 351 | 49% helix, 17% strand | Q9ZTU2 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- CIY · (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal · ligand · 4 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.85 | 0.93 | 67 | SAH, CIY |
| 2 | 376 | 0.84 | 0.93 | 58 | SAH, CIY |
| 3 | 389 | 0.84 | 0.92 | 64 | SAH, CIY |
| 4 | 377 | 0.84 | 0.92 | 64 | SAH, CIY |
| 5 | 219 | 0.58 | 0.80 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4605 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 4547 Ų buried · 71 hydrogen bonds · protein-protein
- B–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3P9K · Crystal structure of perennial ryegrass LpOMT1 complexed with S-adenosyl-L-homocysteine… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9ZTU2
- Elsewhere: RCSB PDB 3P9K · PDBe 3P9K · UniProt Q9ZTU2
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