Research workbench
Crystal structure of a synthase 2 from santalum album in complex with LIGAND1
Analyse Crystal structure of a synthase 2 from santalum album in complex with LIGAND1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A2D
- Type
- protein
- Length
- 1,029 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sesquisabinene B synthase 2
- UniProt
- A0A0A0RCB5
- Ligands
- 6R2, MG
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sesquisabinene B synthase 2 | protein | 519 | 73% helix, 1% strand | A0A0A0RCB5 |
| B | Sesquisabinene B synthase 2 | protein | 510 | 73% helix, 1% strand | A0A0A0RCB5 |
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 · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.79 | 0.81 | 54 | empty |
| 2 | 560 | 0.71 | 0.80 | 63 | 6R2, MG |
| 3 | 372 | 0.71 | 0.83 | 41 | empty |
| 4 | 513 | 0.70 | 0.80 | 55 | 6R2, MG |
| 5 | 362 | 0.70 | 0.82 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1008 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6A2D · Crystal structure of a synthase 2 from santalum album in complex with ligand1 · 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 A0A0A0RCB5
- Elsewhere: RCSB PDB 6A2D · PDBe 6A2D · UniProt A0A0A0RCB5
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