MolNFT v1 · #35363 · protein
S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with bph-629
2E93 · Geranylgeranyl pyrophosphate synthetase: “S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with bph-629”. X-ray diffraction, 1 ligand (B29), 5 pockets (best druggability 0.82). MolNFT v1 #35363 on GenesisL1: 3D…
- PDB
- 2E93
- Type
- protein
- Length
- 613 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
- B29
- Pockets
- 5 · best druggability 0.82
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) | protein | 299 | 77% helix, 1% strand | Q12051 |
| B | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.30) | protein | 314 | 75% helix, 1% strand | Q12051 |
Ligands and binding sites
- B29 · [2-(3-dibenzofuran-4-yl-phenyl)-1-hydroxy-1-phosphono-ethyl]-phosphonic acid · ligand · 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 | 837 | 0.82 | 0.85 | 78 | B29 |
| 2 | 946 | 0.81 | 0.82 | 59 | B29 |
| 3 | 71 | 0.35 | 0.76 | 16 | empty |
| 4 | 64 | 0.32 | 0.74 | 12 | empty |
| 5 | 54 | 0.24 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3438 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2E93 · S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with BPH-629 · 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 0.98
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 2E93 · PDBe 2E93 · UniProt Q12051
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.