MolNFT v1 · #48923 · protein
Crystal structure of human geranylgeranyl pyrophosphate synthase bound to ggpp
2Q80 · Geranylgeranyl pyrophosphate synthetase: “Crystal structure of human geranylgeranyl pyrophosphate synthase bound to ggpp”. X-ray diffraction, 2 ligands (GRG, MG), 20 pockets (best druggability 0.82). MolNFT v1 #48923 on GenesisL1…
- PDB
- 2Q80
- Type
- protein
- Length
- 1,706 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthetase
- EC
- 2.5.1.1, 2.5.1.10, 2.5.1.29
- UniProt
- O95749
- Ligands
- GRG, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.1, 2.5.1.10, 2.5.1.29) | protein | 285 | 76% helix, 1% strand | O95749 |
| B, C, E, F | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.1, 2.5.1.10, 2.5.1.29) | protein | 284 | 75% helix, 1% strand | O95749 |
| D | Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.1, 2.5.1.10, 2.5.1.29) | protein | 285 | 76% helix, 1% strand | O95749 |
Ligands and binding sites
- GRG · Geranylgeranyl diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.82 | 0.86 | 62 | MG, GRG |
| 2 | 697 | 0.81 | 0.85 | 57 | MG, GRG |
| 3 | 735 | 0.81 | 0.85 | 61 | MG, GRG |
| 4 | 671 | 0.81 | 0.85 | 60 | GRG |
| 5 | 701 | 0.81 | 0.85 | 56 | MG, GRG |
Interfaces
12 interfaces between chains.
- A–B · 1626 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1611 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1604 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 530 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 519 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2Q80 · Crystal structure of human geranylgeranyl pyrophosphate synthase bound to GGPP · the same entry in another collection · chain F against F, TM-score 1.00
- O95749 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase (O95749) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O95749
- Elsewhere: RCSB PDB 2Q80 · PDBe 2Q80 · UniProt O95749
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.