MolNFT v1 · #124749 · protein
Pavine N-methyltransferase in complex with S-adenosylmethionine pH 7
5KOC: “Pavine N-methyltransferase in complex with S-adenosylmethionine pH 7”. X-ray diffraction, 1 ligand (SAM), 5 pockets (best druggability 0.79). MolNFT v1 #124749 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KOC
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pavine N-methyltransferase
- EC
- 2.1.1.300
- UniProt
- C3SBW0
- Ligands
- SAM
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pavine N-methyltransferase (EC 2.1.1.300) | protein | 338 | 48% helix, 18% strand | C3SBW0 |
| B | Pavine N-methyltransferase (EC 2.1.1.300) | protein | 336 | 49% helix, 18% strand | C3SBW0 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.79 | 0.80 | 76 | SAM |
| 2 | 770 | 0.77 | 0.81 | 70 | SAM |
| 3 | 358 | 0.72 | 0.84 | 32 | empty |
| 4 | 58 | 0.38 | 0.79 | 15 | empty |
| 5 | 54 | 0.31 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1066 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5KOC · Pavine N-methyltransferase in complex with S-adenosylmethionine pH 7 · the same entry in another collection · chain A against A, TM-score 1.00
- C3SBW0 · AlphaFold monomer V2.0 prediction for pavine N-methyltransferase (C3SBW0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 C3SBW0
- Elsewhere: RCSB PDB 5KOC · PDBe 5KOC · UniProt C3SBW0
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