MolNFT v1 · #56186 · protein
S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with bph-806
2Z78 · Geranylgeranyl pyrophosphate synthetase: “S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with bph-806”. X-ray diffraction, 1 ligand (H86), 7 pockets (best druggability 0.82). MolNFT v1 #56186 on GenesisL1: 3D…
- PDB
- 2Z78
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthetase
- EC
- 2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29
- UniProt
- Q12051
- Ligands
- H86
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29) | protein | 321 | 75% helix, 1% strand | Q12051 |
| B | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29) | protein | 317 | 75% helix, 1% strand | Q12051 |
Ligands and binding sites
- H86 · 3-(decyloxy)-5-(3,5-difluorophenyl)-1-(2,2-diphosphonoethyl)pyridinium · ligand · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.82 | 0.86 | 68 | H86 |
| 2 | 621 | 0.81 | 0.86 | 57 | H86 |
| 3 | 69 | 0.32 | 0.75 | 13 | empty |
| 4 | 77 | 0.32 | 0.74 | 17 | empty |
| 5 | 62 | 0.28 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3433 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2Z78 · S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-806 · the same entry in another collection · chain A against A, TM-score 1.00
- Q12051 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase (Q12051) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q12051
- Elsewhere: RCSB PDB 2Z78 · PDBe 2Z78 · UniProt Q12051
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