MolNFT v1 · #124781 · protein
Pavine N-methyltransferase H206A mutant in complex with S- adenosylmethionine pH 6
5KPC: “Pavine N-methyltransferase H206A mutant in complex with S- adenosylmethionine pH 6”. X-ray diffraction, 1 ligand (SAM), 7 pockets (best druggability 0.75). MolNFT v1 #124781 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5KPC
- Type
- protein
- Length
- 657 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
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pavine N-methyltransferase (EC 2.1.1.300) | protein | 335 | 49% helix, 19% strand | C3SBW0 |
| B | Pavine N-methyltransferase (EC 2.1.1.300) | protein | 322 | 47% helix, 19% 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.75 | 0.80 | 67 | SAM |
| 2 | 744 | 0.75 | 0.80 | 66 | SAM |
| 3 | 396 | 0.73 | 0.84 | 35 | empty |
| 4 | 98 | 0.41 | 0.77 | 21 | empty |
| 5 | 67 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1109 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5KPC · Pavine N-methyltransferase H206A mutant in complex with S-adenosylmethionine pH 6 · 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 B 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 5KPC · PDBe 5KPC · UniProt C3SBW0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.