MolNFT v1 · #154406 · protein
Crystal structure of a thebaine synthase from papaver somniferum
6KA3 · Thebaine synthase 2: “Crystal structure of a thebaine synthase from papaver somniferum”. X-ray diffraction, 2 ligands (PLM, SO4), 7 pockets (best druggability 0.85). MolNFT v1 #154406 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6KA3
- Type
- protein
- Length
- 601 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thebaine synthase 2
- EC
- 4.2.99.24
- UniProt
- A0A2U9GGW3
- Ligands
- PLM, SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thebaine synthase 2 (EC 4.2.99.24) | protein | 151 | 26% helix, 47% strand | A0A2U9GGW3 |
| C | Thebaine synthase 2 (EC 4.2.99.24) | protein | 150 | 25% helix, 47% strand | A0A2U9GGW3 |
| D | Thebaine synthase 2 (EC 4.2.99.24) | protein | 149 | 25% helix, 47% strand | A0A2U9GGW3 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.85 | 0.97 | 26 | PLM |
| 2 | 220 | 0.85 | 0.97 | 27 | empty |
| 3 | 220 | 0.85 | 0.97 | 26 | PLM |
| 4 | 449 | 0.81 | 0.89 | 55 | empty |
| 5 | 876 | 0.75 | 0.79 | 72 | SO4 |
Interfaces
5 interfaces between chains.
- C–D · 901 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 895 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 116 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 90 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KA3 · Crystal structure of a Thebaine synthase from Papaver somniferum · 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 A0A2U9GGW3
- Elsewhere: RCSB PDB 6KA3 · PDBe 6KA3 · UniProt A0A2U9GGW3
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