MolNFT v1 · #116762 · protein
The structure of PKMT1 from rickettsia prowazekii in complex with adohcy
5DNK · Protein lysine methyltransferase 1: “The structure of PKMT1 from rickettsia prowazekii in complex with adohcy”. X-ray diffraction, 1 ligand (SAH), 15 pockets (best druggability 0.68). MolNFT v1 #116762 on GenesisL1: 3D structure…
- PDB
- 5DNK
- Type
- protein
- Length
- 1,012 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein lysine methyltransferase 1
- UniProt
- O05979
- Ligands
- SAH
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein lysine methyltransferase 1 | protein | 510 | 49% helix, 16% strand | O05979 |
| B | Protein lysine methyltransferase 1 | protein | 502 | 47% helix, 16% strand | O05979 |
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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.68 | 0.79 | 48 | empty |
| 2 | 346 | 0.67 | 0.81 | 45 | empty |
| 3 | 574 | 0.64 | 0.75 | 49 | SAH |
| 4 | 552 | 0.63 | 0.75 | 48 | SAH |
| 5 | 246 | 0.61 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1688 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5DNK · The structure of PKMT1 from Rickettsia prowazekii in complex with AdoHcy · the same entry in another collection · chain A against A, TM-score 1.00
- O05979 · AlphaFold monomer V2.0 prediction for uncharacterized protein RP789 (O05979) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O05979
- Elsewhere: RCSB PDB 5DNK · PDBe 5DNK · UniProt O05979
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