MolNFT v1 · #46833 · protein
T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-527
2OGD · Farnesyl pyrophosphate synthase: “T. brucei farnesyl diphosphate synthase complexed with bisphosphonate bph-527”. X-ray diffraction, 2 ligands (SUF, MG), 7 pockets (best druggability 0.81). MolNFT v1 #46833 on GenesisL1: 3D…
- PDB
- 2OGD
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10
- UniProt
- Q86C09
- Ligands
- SUF, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 358 | 73% helix, 1% strand | Q86C09 |
| B | Farnesyl pyrophosphate synthase (EC 2.5.1.10) | protein | 359 | 74% helix, 1% strand | Q86C09 |
Ligands and binding sites
- SUF · [2-(dimethyl-lambda~4~-sulfanyl)-1-hydroxyethane-1,1-diyl]bis(phosphonic acid) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.81 | 0.93 | 45 | ACT, MG, SUF |
| 2 | 301 | 0.79 | 0.90 | 47 | ACT, MG, SUF |
| 3 | 68 | 0.62 | 0.91 | 19 | empty |
| 4 | 101 | 0.43 | 0.78 | 14 | MPD |
| 5 | 92 | 0.42 | 0.78 | 15 | BME |
Interfaces
1 interface between chains.
- A–B · 3138 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 2OGD · T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-527 · 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 Q86C09
- Elsewhere: RCSB PDB 2OGD · PDBe 2OGD · UniProt Q86C09
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