MolNFT v1 · #167882 · protein
Terpenoid cyclase fggs in complex with mg, inorganic pyrophosphate, and benzyltriethylammonium cation
6VYD: “Terpenoid cyclase fggs in complex with mg, inorganic pyrophosphate, and benzyltriethylammonium cation”. X-ray diffraction, 6 ligands (POP, BTM, MG), 9 pockets (best druggability 0.83). MolNFT v1 #167882 on GenesisL1: 3D structure…
- PDB
- 6VYD
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terpenoid cyclase fggs
- UniProt
- I1RDR8
- Ligands
- POP, BTM, MG, NA, CL, SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terpenoid cyclase fggs | protein | 304 | 70% helix, 3% strand | I1RDR8 |
| B | Terpenoid cyclase fggs | protein | 291 | 70% helix, 3% strand | I1RDR8 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- BTM · N-benzyl-N,N-diethylethanaminium · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.83 | 0.96 | 32 | POP, BTM, EDO |
| 2 | 233 | 0.83 | 0.96 | 33 | MG, POP, BTM, EDO |
| 3 | 435 | 0.65 | 0.78 | 47 | EDO |
| 4 | 320 | 0.56 | 0.76 | 41 | NA, EDO |
| 5 | 138 | 0.53 | 0.81 | 22 | EDO |
Interfaces
1 interface between chains.
- A–B · 625 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6VYD · Terpenoid Cyclase FgGS in Complex with Mg, Inorganic Pyrophosphate, 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 I1RDR8
- Elsewhere: RCSB PDB 6VYD · PDBe 6VYD · UniProt I1RDR8
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