Research workbench
S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and bph-23
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
- 2Z52
- Type
- protein
- Length
- 592 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
- H23, MG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 77% 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 | 296 | 76% 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 | 77% helix, 1% strand | Q12051 |
Ligands and binding sites
- H23 · (1-hydroxydodecane-1,1-diyl)bis(phosphonic acid) · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 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 | 633 | 0.77 | 0.83 | 52 | H23, MG |
| 2 | 607 | 0.74 | 0.81 | 54 | H23, MG |
| 3 | 105 | 0.34 | 0.73 | 26 | empty |
| 4 | 50 | 0.33 | 0.78 | 15 | empty |
| 5 | 70 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3492 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2Z52 · S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-23 · the same entry in another collection · chain B against B, 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 2Z52 · PDBe 2Z52 · UniProt Q12051
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