MolNFT v1 · #152051 · protein
Papaver somniferum O-methyltransferase
6I5Z · O-methyltransferase 1: “Papaver somniferum O-methyltransferase”. X-ray diffraction, 2 ligands (SAH, SAM), 14 pockets (best druggability 0.78). MolNFT v1 #152051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6I5Z
- Type
- protein
- Length
- 1,380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase 1
- UniProt
- I3PLQ5
- Ligands
- SAH, SAM
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | O-methyltransferase 1 | protein | 342 | 49% helix, 13% strand | I3PLQ5 |
| B | O-methyltransferase 1 | protein | 349 | 47% helix, 15% strand | I3PLQ5 |
| D | O-methyltransferase 1 | protein | 347 | 45% helix, 13% strand | I3PLQ5 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.78 | 0.80 | 75 | SAH |
| 2 | 807 | 0.75 | 0.79 | 59 | SAH |
| 3 | 810 | 0.74 | 0.78 | 54 | SAM |
| 4 | 721 | 0.71 | 0.78 | 58 | empty |
| 5 | 51 | 0.70 | 0.98 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–D · 4131 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 4109 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 525 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6I5Z · Papaver somniferum O-methyltransferase · 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 I3PLQ5
- Elsewhere: RCSB PDB 6I5Z · PDBe 6I5Z · UniProt I3PLQ5
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