MolNFT v1 · #36481 · protein
Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase complexed with sn-G1P and mpd
2F6X: “Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase complexed with sn-G1P and mpd”. X-ray diffraction, 1 ligand (1GP), 4 pockets (best druggability 0.79). MolNFT v1 #36481 on GenesisL1: 3D structure, binding sites…
- PDB
- 2F6X
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (S)-3-O-geranylgeranylglyceryl phosphate synthase
- EC
- 2.5.1.42
- UniProt
- O29844
- Ligands
- 1GP
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | (S)-3-O-geranylgeranylglyceryl phosphate synthase (EC 2.5.1.42) | protein | 231 | 40% helix, 19% strand | O29844 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.79 | 0.85 | 68 | 1GP, MPD |
| 2 | 558 | 0.79 | 0.85 | 58 | 1GP, MPD |
| 3 | 117 | 0.42 | 0.77 | 20 | empty |
| 4 | 107 | 0.40 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1529 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2F6X · Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- O29844 · AlphaFold monomer V2.0 prediction for geranylgeranylglyceryl phosphate synthase (O29844) · 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 O29844
- Elsewhere: RCSB PDB 2F6X · PDBe 2F6X · UniProt O29844
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