Research workbench
Crystal structure of geranylgeranyl pyrophosphate synthase from lactobacillus brevis atcc 367 complexed with citrate
Analyse Crystal structure of geranylgeranyl pyrophosphate synthase from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PKO
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthase
- UniProt
- Q03Q08
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthase | protein | 331 | 74% helix, 1% strand | Q03Q08 |
| B | Geranylgeranyl pyrophosphate synthase | protein | 310 | 77% helix, 0% strand | Q03Q08 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.77 | 0.83 | 58 | CIT |
| 2 | 658 | 0.72 | 0.79 | 65 | empty |
| 3 | 53 | 0.63 | 0.94 | 21 | empty |
| 4 | 63 | 0.31 | 0.75 | 17 | empty |
| 5 | 52 | 0.29 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 2030 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3PKO · Crystal structure of geranylgeranyl pyrophosphate synthase from lactobacillus brevis atcc… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q03Q08
- Elsewhere: RCSB PDB 3PKO · PDBe 3PKO · UniProt Q03Q08
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