Research workbench
Crystal structure of the indole prenyltransferase MpnD complexed with indolactam V and DMSPP
Analyse Crystal structure of the indole prenyltransferase MpnD complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YLA
- Type
- protein
- Length
- 374 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Marinactinospora thermotolerans
- Molecule
- Aromatic prenyltransferase
- UniProt
- I7EIW6
- Ligands
- ILV, DST, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.4 · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic prenyltransferase | protein | 374 | 34% helix, 20% strand | I7EIW6 |
Ligands and binding sites
- ILV · (2S,5S)-5-(hydroxymethyl)-1-methyl-2-(propan-2-yl)-1,2,4,5,6,8-hexahydro-3H-[1,4]diazonino[7,6,5-cd]indol-3-one · ligand · chains A
- DST · Dimethylallyl S-thiolodiphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.77 | 0.87 | 43 | ILV, DST |
| 2 | 393 | 0.71 | 0.83 | 44 | DST |
| 3 | 53 | 0.46 | 0.84 | 19 | empty |
| 4 | 71 | 0.42 | 0.81 | 19 | empty |
| 5 | 59 | 0.41 | 0.81 | 21 | empty |
Compared structures
- 4YLA · Crystal structure of the indole prenyltransferase mpnd complexed with indolactam V and… · 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 I7EIW6
- Elsewhere: RCSB PDB 4YLA · PDBe 4YLA · UniProt I7EIW6
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