MolNFT v1 · #135268 · protein
Pagf prenyltransferase with CYCLIC[INPYLYP] and dmspp
5TU6: “Pagf prenyltransferase with CYCLIC[INPYLYP] and dmspp”. X-ray diffraction, 3 ligands (MET, DST, MG), 4 pockets (best druggability 0.68). MolNFT v1 #135268 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5TU6
- Type
- protein
- Length
- 303 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pagf prenyltransferase; CYCLIC[INPYLYP] peptide
- UniProt
- F5B6Z0
- Ligands
- MET, DST, MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pagf prenyltransferase | protein | 296 | 42% helix, 29% strand | F5B6Z0 |
| B | CYCLIC[INPYLYP] peptide | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- MET · Methionine · ligand · chains A
- DST · Dimethylallyl S-thiolodiphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.68 | 0.84 | 45 | MG, DST |
| 2 | 94 | 0.49 | 0.81 | 18 | empty |
| 3 | 52 | 0.38 | 0.81 | 20 | empty |
| 4 | 78 | 0.31 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5TU6 · PagF prenyltransferase with cyclic[INPYLYP] and DMSPP · 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 F5B6Z0
- Elsewhere: RCSB PDB 5TU6 · PDBe 5TU6 · UniProt F5B6Z0
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