MolNFT v1 · #116717 · protein
Crystal structure of the plantazolicin methyltransferase bpuml in complex with pentazolic desmethylpzn analog and sah
5DM4 · Methyltransferase domain family: “Crystal structure of the plantazolicin methyltransferase bpuml in complex with pentazolic desmethylpzn analog…”. X-ray diffraction, 2 ligands (SAH, 5DA), 1 pocket (best druggability 0.79). MolNFT v1…
- PDB
- 5DM4
- Type
- protein
- Length
- 257 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase domain family
- UniProt
- B4ADV2
- Ligands
- SAH, 5DA
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase domain family | protein | 257 | 52% helix, 20% strand | B4ADV2 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- 5DA · 1-[(4S)-4-(4-{4-[4-(5,5'-dimethyl-2,4'-bi-1,3-oxazol-2'-yl)-1,3-thiazol-2-yl]-5-methyl-1,3-oxazol-2-yl}-1,3-thiazol-2-yl)-4-(methylamino)butyl]guanidine · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.79 | 0.85 | 72 | SAH, GOL, 5DA |
Compared structures
- 5DM4 · Crystal structure of the plantazolicin methyltransferase BpumL in complex with pentazolic… · 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 B4ADV2
- Elsewhere: RCSB PDB 5DM4 · PDBe 5DM4 · UniProt B4ADV2
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