MolNFT v1 · #189605 · protein
Crystal structure of limf prenyltransferase bound with gspp
7VMY · LYNF/TRUF/PATF family peptide O-prenyltransferase: “Crystal structure of limf prenyltransferase bound with gspp”. X-ray diffraction, 2 ligands (GST, MG), 4 pockets (best druggability 0.79). MolNFT v1 #189605 on GenesisL1: 3D…
- PDB
- 7VMY
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYNF/TRUF/PATF family peptide O-prenyltransferase
- UniProt
- A0A372DCN7
- Ligands
- GST, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYNF/TRUF/PATF family peptide O-prenyltransferase | protein | 294 | 36% helix, 31% strand | A0A372DCN7 |
| B | LYNF/TRUF/PATF family peptide O-prenyltransferase | protein | 295 | 37% helix, 29% strand | A0A372DCN7 |
Ligands and binding sites
- GST · Geranyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.79 | 0.80 | 102 | MG, GST, BTB |
| 2 | 1197 | 0.78 | 0.80 | 123 | MG, GST, BTB |
| 3 | 54 | 0.34 | 0.78 | 15 | empty |
| 4 | 52 | 0.33 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7VMY · Crystal structure of LimF prenyltransferase bound with GSPP · 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 A0A372DCN7
- Elsewhere: RCSB PDB 7VMY · PDBe 7VMY · UniProt A0A372DCN7
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