Research workbench
Crystal structure of the plantazolicin methyltransferase bpuml in complex with pentazolic desmethylpzn analog and sah
Analyse Crystal structure of the plantazolicin methyltransferase bpuml in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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