MolNFT v1 · #152087 · protein
Structure of fragaria ananassa O-methyltransferase in complex with S- adenosylhomocysteine and caffeic acid
6I72: “Structure of fragaria ananassa O-methyltransferase in complex with S- adenosylhomocysteine and caffeic acid”. X-ray diffraction, 3 ligands (SAH, DHC, SO4), 11 pockets (best druggability 0.84). MolNFT v1 #152087 on GenesisL1: 3D…
- PDB
- 6I72
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase
- UniProt
- Q9M602
- Ligands
- SAH, DHC, SO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-methyltransferase | protein | 352 | 48% helix, 17% strand | Q9M602 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- DHC · Caffeic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.84 | 0.93 | 64 | SAH, DHC |
| 2 | 321 | 0.84 | 0.93 | 61 | SAH, DHC |
| 3 | 274 | 0.58 | 0.78 | 45 | empty |
| 4 | 194 | 0.57 | 0.80 | 32 | EDO |
| 5 | 186 | 0.53 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 4363 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6I72 · Structure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine… · 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 Q9M602
- Elsewhere: RCSB PDB 6I72 · PDBe 6I72 · UniProt Q9M602
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