MolNFT v1 · #143453 · protein
Crystal structure of CFFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with [2-(1-methylpyridin-2-yl)-1- phosphono-ETHYL]PHOSPHONIC acid (inhibitor 1B)
6B04: “Crystal structure of CFFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with…”. X-ray diffraction, 2 ligands (C6J, MG), 10 pockets (best druggability 0.83). MolNFT v1 #143453 on GenesisL1: 3D structure, binding…
- PDB
- 6B04
- Type
- protein
- Length
- 1,014 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl diphosphate synthase
- EC
- 2.5.1.-
- UniProt
- Q1XAB1
- Ligands
- C6J, MG
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl diphosphate synthase (EC 2.5.1.-) | protein | 341 | 76% helix, 2% strand | Q1XAB1 |
| B | Farnesyl diphosphate synthase (EC 2.5.1.-) | protein | 338 | 75% helix, 2% strand | Q1XAB1 |
| C | Farnesyl diphosphate synthase (EC 2.5.1.-) | protein | 335 | 75% helix, 1% strand | Q1XAB1 |
Ligands and binding sites
- C6J · [2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 9 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.83 | 0.89 | 64 | C6J, MG |
| 2 | 372 | 0.82 | 0.91 | 50 | C6J, MG |
| 3 | 597 | 0.79 | 0.85 | 67 | C6J, MG, EDO |
| 4 | 224 | 0.56 | 0.78 | 33 | empty |
| 5 | 215 | 0.55 | 0.78 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2024 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 694 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6B04 · Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase… · 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 Q1XAB1
- Elsewhere: RCSB PDB 6B04 · PDBe 6B04 · UniProt Q1XAB1
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