MolNFT v1 · #154501 · protein
Crystal structure of geranylgeranyl pyrophosphate synthase
6KD7 · Polyprenyl synthetase: “Crystal structure of geranylgeranyl pyrophosphate synthase”. X-ray diffraction, 2 ligands (PPV, MG), 2 pockets (best druggability 0.76). MolNFT v1 #154501 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6KD7
- Type
- protein
- Length
- 327 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprenyl synthetase
- UniProt
- L7W5I6
- Ligands
- PPV, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprenyl synthetase | protein | 327 | 73% helix, 1% strand | L7W5I6 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.76 | 0.79 | 73 | PPV, GOL, MG |
| 2 | 50 | 0.27 | 0.74 | 14 | empty |
Compared structures
- 6KD7 · Crystal structure of geranylgeranyl pyrophosphate synthase · 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 L7W5I6
- Elsewhere: RCSB PDB 6KD7 · PDBe 6KD7 · UniProt L7W5I6
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