Research workbench
S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and bph-749
Analyse S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z4W
- Type
- protein
- Length
- 588 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
- 749, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 76% 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 | 292 | 77% 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 | 296 | 75% helix, 1% strand | Q12051 |
Ligands and binding sites
- 749 · [(6E,11E)-2,6,12,16-tetramethylheptadeca-2,6,11,15-tetraene-9,9-diyl]bis(phosphonic acid) · ligand · 2 copies · chains A, 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.77 | 0.81 | 61 | 749, MG |
| 2 | 532 | 0.71 | 0.80 | 54 | 749, MG |
| 3 | 65 | 0.34 | 0.76 | 11 | empty |
| 4 | 63 | 0.32 | 0.76 | 15 | empty |
| 5 | 60 | 0.30 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 3379 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2Z4W · S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-749 · 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 A against A, TM-score 0.97
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 2Z4W · PDBe 2Z4W · UniProt Q12051
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