MolNFT v1 · #56424 · protein
S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium, ipp and bph-715
2ZEV · Geranylgeranyl pyrophosphate synthetase: “S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium, ipp and bph-715”. X-ray diffraction, 3 ligands (B71, IPE, MG), 5 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 2ZEV
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthetase
- EC
- 2.5.1.30
- UniProt
- Q12051
- Ligands
- B71, IPE, MG
- Pockets
- 5 · best druggability 0.76
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) | protein | 298 | 75% helix, 1% strand | Q12051 |
| B | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.30) | protein | 299 | 75% helix, 1% strand | Q12051 |
Ligands and binding sites
- B71 · 3-(decyloxy)-1-(2,2-diphosphonoethyl)pyridinium · ligand · 2 copies · chains A, B
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.76 | 0.81 | 57 | MG, IPE, B71 |
| 2 | 447 | 0.71 | 0.82 | 44 | MG, B71 |
| 3 | 70 | 0.35 | 0.76 | 15 | empty |
| 4 | 53 | 0.30 | 0.75 | 11 | empty |
| 5 | 67 | 0.28 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3390 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2ZEV · S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, IPP and… · 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 0.98
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 2ZEV · PDBe 2ZEV · UniProt Q12051
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