MolNFT v1 · #92983 · protein
Crystal structure of isoprenoid synthase A3MSH1 (target efi-501992) from pyrobaculum calidifontis complexed with dmapp and magnesium
4GP2 · Polyprenyl synthetase: “Crystal structure of isoprenoid synthase A3MSH1 (target efi-501992) from pyrobaculum calidifontis complexed…”. X-ray diffraction, 2 ligands (DMA, MG), 2 pockets (best druggability 0.73). MolNFT v1 #92983 on…
- PDB
- 4GP2
- Type
- protein
- Length
- 673 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprenyl synthetase
- UniProt
- A3MSH1
- Ligands
- DMA, MG
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprenyl synthetase | protein | 342 | 74% helix, 2% strand | A3MSH1 |
| B | Polyprenyl synthetase | protein | 331 | 76% helix, 2% strand | A3MSH1 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.73 | 0.79 | 70 | MG, DMA |
| 2 | 461 | 0.72 | 0.82 | 54 | MG, DMA |
Interfaces
1 interface between chains.
- A–B · 2131 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4GP2 · Crystal structure of ISOPRENOID SYNTHASE A3MSH1 (TARGET EFI-501992) from pyrobaculum… · 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 A3MSH1
- Elsewhere: RCSB PDB 4GP2 · PDBe 4GP2 · UniProt A3MSH1
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