Research workbench
Crystal structure of isoflavone O-methyltransferase homolog in complex with biochanin a and sah
Analyse Crystal structure of isoflavone O-methyltransferase homolog in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QYO
- Type
- protein
- Length
- 705 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase
- EC
- 2.1.1.46
- UniProt
- Q1SCE3
- Ligands
- SAH, QSO, K
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-methyltransferase (EC 2.1.1.46) | protein | 353 | 50% helix, 15% strand | Q1SCE3 |
| B | O-methyltransferase (EC 2.1.1.46) | protein | 352 | 51% helix, 15% strand | Q1SCE3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- QSO · 5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.76 | 0.80 | 62 | K, SAH, QSO |
| 2 | 827 | 0.75 | 0.79 | 57 | SAH, QSO |
| 3 | 599 | 0.67 | 0.77 | 71 | empty |
| 4 | 362 | 0.59 | 0.77 | 45 | K |
| 5 | 88 | 0.41 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 4974 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 2QYO · Crystal structure of isoflavone O-methyltransferase homolog in complex with biochanin A… · 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 Q1SCE3
- Elsewhere: RCSB PDB 2QYO · PDBe 2QYO · UniProt Q1SCE3
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