MolNFT v1 · #142344 · protein
Crystal structure of a synthase 1 from santalum album in complex with ligand
6A1D · Sesquisabinene B synthase 1: “Crystal structure of a synthase 1 from santalum album in complex with ligand”. X-ray diffraction, 3 ligands (6R2, MG, SO4), 7 pockets (best druggability 0.73). MolNFT v1 #142344 on GenesisL1: 3D…
- PDB
- 6A1D
- Type
- protein
- Length
- 516 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sesquisabinene B synthase 1
- UniProt
- A0A0A0RDR2
- Ligands
- 6R2, MG, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sesquisabinene B synthase 1 | protein | 516 | 74% helix, 0% strand | A0A0A0RDR2 |
Ligands and binding sites
- 6R2 · [bis(chloranyl)-[oxidanyl-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]phosphoryl]methyl]phosphonic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.73 | 0.88 | 27 | empty |
| 2 | 334 | 0.71 | 0.84 | 40 | empty |
| 3 | 356 | 0.66 | 0.80 | 46 | 6R2, MG |
| 4 | 209 | 0.57 | 0.79 | 20 | empty |
| 5 | 103 | 0.41 | 0.76 | 13 | empty |
Compared structures
- 6A1D · Crystal structure of a synthase 1 from Santalum album in complex with ligand · 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 A0A0A0RDR2
- Elsewhere: RCSB PDB 6A1D · PDBe 6A1D · UniProt A0A0A0RDR2
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