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Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium glutamicum complexed with isoprenyl diphosphate and magnesium
Analyse Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QQV
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthase
- EC
- 2.5.1.1
- UniProt
- Q8NNM1
- Ligands
- DMA, UNL, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthase (EC 2.5.1.1) | protein | 357 | 78% helix, 1% strand | Q8NNM1 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 2 copies · chains A
- UNL · Unknown ligand · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.78 | 0.86 | 48 | MG, DMA |
| 2 | 88 | 0.48 | 0.82 | 18 | empty |
| 3 | 56 | 0.34 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3QQV · Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium… · 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 Q8NNM1
- Elsewhere: RCSB PDB 3QQV · PDBe 3QQV · UniProt Q8NNM1
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