MolNFT v1 · #35365 · protein
S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and bph-675
2E95 · Geranylgeranyl pyrophosphate synthetase: “S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and bph-675”. X-ray diffraction, 2 ligands (B75, MG), 8 pockets (best druggability 0.82). MolNFT v1 #35365 on…
- PDB
- 2E95
- Type
- protein
- Length
- 627 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
- B75, MG
- Pockets
- 8 · 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) | protein | 316 | 76% helix, 1% strand | Q12051 |
| B | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.30) | protein | 311 | 74% helix, 1% strand | Q12051 |
Ligands and binding sites
- B75 · 1-hydroxy-2-[3'-(naphthalene-2-sulfonylamino)-biphenyl-3-yl]ethylidene-1,1-bisphosphonic 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.82 | 0.85 | 66 | MG, B75 |
| 2 | 736 | 0.81 | 0.85 | 64 | MG, B75 |
| 3 | 105 | 0.57 | 0.84 | 18 | empty |
| 4 | 95 | 0.41 | 0.77 | 14 | empty |
| 5 | 59 | 0.34 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 3477 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2E95 · S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-675 · 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 0.96
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 2E95 · PDBe 2E95 · UniProt Q12051
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