MolNFT v1 · #168167 · protein
Lmfpps mutant T164W in complex with 476A, ipp & ca
6W7I · Farnesyl pyrophosphate synthase: “Lmfpps mutant T164W in complex with 476A, ipp & ca”. X-ray diffraction, 3 ligands (IPR, 476, CA), 8 pockets (best druggability 0.83). MolNFT v1 #168167 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6W7I
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.1, 2.5.1.10
- UniProt
- Q4QBL1
- Ligands
- IPR, 476, CA
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Farnesyl pyrophosphate synthase (EC 2.5.1.1, 2.5.1.10) | protein | 362 | 74% helix, 2% strand | Q4QBL1 |
Ligands and binding sites
- IPR · Isopentyl pyrophosphate · ligand · 2 copies · chains A, B
- 476 · 3-butyl-1-(2,2-diphosphonoethyl)pyridinium · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.83 | 0.93 | 51 | CA, IPR, 476, PEG |
| 2 | 366 | 0.82 | 0.91 | 60 | CA, IPR, 476 |
| 3 | 110 | 0.47 | 0.79 | 23 | empty |
| 4 | 121 | 0.46 | 0.78 | 23 | empty |
| 5 | 101 | 0.41 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2960 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (formylation).
Compared structures
- 6W7I · LmFPPS mutant T164W in complex with 476A, IPP & Ca · 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 Q4QBL1
- Elsewhere: RCSB PDB 6W7I · PDBe 6W7I · UniProt Q4QBL1
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