MolNFT v1 · #116713 · protein
Crystal structure of the plantazolicin methyltransferase baml in complex with triazolic desmethylpzn analog and sah
5DM0: “Crystal structure of the plantazolicin methyltransferase baml in complex with triazolic desmethylpzn analog…”. X-ray diffraction, 3 ligands (SAH, 5D8, SO4), 2 pockets (best druggability 0.86). MolNFT v1 #116713 on GenesisL1: 3D…
- PDB
- 5DM0
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plantazolicin methyltransferase baml
- UniProt
- A7Z2A9
- Ligands
- SAH, 5D8, SO4
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plantazolicin methyltransferase baml | protein | 266 | 55% helix, 19% strand | A7Z2A9 |
| B | Plantazolicin methyltransferase baml | protein | 272 | 52% helix, 18% strand | A7Z2A9 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- 5D8 · ethyl 2-(2-{2-[(1S)-1-amino-4-carbamimidamidobutyl]-1,3-thiazol-4-yl}-5-methyl-1,3-oxazol-4-yl)-1,3-thiazole-4-carboxylate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.86 | 0.87 | 125 | SAH, 5D8 |
| 2 | 586 | 0.83 | 0.88 | 69 | SAH, 5D8 |
Interfaces
1 interface between chains.
- A–B · 660 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5DM0 · Crystal structure of the plantazolicin methyltransferase BamL in complex with triazolic… · 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 A7Z2A9
- Elsewhere: RCSB PDB 5DM0 · PDBe 5DM0 · UniProt A7Z2A9
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