MolNFT v1 · #124785 · protein
Pavine N-methyltransferase in complex with S-adenosylhomocysteine pH 7
5KPG: “Pavine N-methyltransferase in complex with S-adenosylhomocysteine pH 7”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.77). MolNFT v1 #124785 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KPG
- Type
- protein
- Length
- 677 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
- SAH
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pavine N-methyltransferase (EC 2.1.1.300) | protein | 339 | 49% helix, 18% strand | C3SBW0 |
| B | Pavine N-methyltransferase (EC 2.1.1.300) | protein | 338 | 49% helix, 18% strand | C3SBW0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · 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 | 737 | 0.77 | 0.81 | 74 | SAH |
| 2 | 708 | 0.76 | 0.81 | 72 | SAH |
| 3 | 382 | 0.72 | 0.84 | 33 | empty |
| 4 | 51 | 0.34 | 0.78 | 16 | empty |
| 5 | 58 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5KPG · Pavine N-methyltransferase in complex with S-adenosylhomocysteine pH 7 · the same entry in another collection · chain B against B, 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 5KPG · PDBe 5KPG · UniProt C3SBW0
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