Research workbench
Crystal structure of geranylgeranyl pyrophosphate synthase from lactobacillus brevis atcc 367
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
- 3N3D
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthase
- UniProt
- Q03Q08
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthase | protein | 322 | 76% helix, 1% strand | Q03Q08 |
| B | Geranylgeranyl pyrophosphate synthase | protein | 313 | 74% helix, 0% strand | Q03Q08 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.73 | 0.81 | 55 | SO4 |
| 2 | 53 | 0.70 | 0.97 | 17 | empty |
| 3 | 501 | 0.64 | 0.76 | 57 | SO4 |
| 4 | 50 | 0.25 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2176 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3N3D · 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 3N3D · PDBe 3N3D · UniProt Q03Q08
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