MolNFT v1 · #116820 · protein
The structure of PKMT2 from rickettsia typhi in complex with adohcy
5DPL · Protein lysine methyltransferase 2: “The structure of PKMT2 from rickettsia typhi in complex with adohcy”. X-ray diffraction, 1 ligand (SAH), 15 pockets (best druggability 0.73). MolNFT v1 #116820 on GenesisL1: 3D structure, binding…
- PDB
- 5DPL
- Type
- protein
- Length
- 1,032 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein lysine methyltransferase 2
- UniProt
- Q68XQ5
- Ligands
- SAH
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein lysine methyltransferase 2 | protein | 520 | 43% helix, 12% strand | Q68XQ5 |
| B | Protein lysine methyltransferase 2 | protein | 512 | 41% helix, 14% strand | Q68XQ5 |
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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.73 | 0.79 | 67 | SAH |
| 2 | 747 | 0.72 | 0.78 | 68 | SAH |
| 3 | 51 | 0.68 | 0.97 | 13 | empty |
| 4 | 318 | 0.62 | 0.79 | 41 | empty |
| 5 | 175 | 0.62 | 0.83 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1635 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DPL · The structure of PKMT2 from Rickettsia typhi in complex with AdoHcy · 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 Q68XQ5
- Elsewhere: RCSB PDB 5DPL · PDBe 5DPL · UniProt Q68XQ5
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