Research workbench
Pagf with boc-tyr and dmspp
Analyse Pagf with boc-tyr and dmspp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TU4
- Type
- protein
- Length
- 297 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pagf prenyltransferase
- UniProt
- F5B6Z0
- Ligands
- DST, B1C, MG
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pagf prenyltransferase | protein | 297 | 42% helix, 29% strand | F5B6Z0 |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · chains A
- B1C · N-(tert-butoxycarbonyl)-L-tyrosine · ligand · chains A
- MG · Magnesium ion · metal · 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 | 469 | 0.72 | 0.82 | 57 | DST, MG, B1C |
Compared structures
- 5TU4 · PagF with Boc-Tyr 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 5TU4 · PDBe 5TU4 · UniProt F5B6Z0
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