Research workbench
Crystal structure of a thebaine synthase from papaver somniferum in complex with tbn
Analyse Crystal structure of a thebaine synthase from papaver somniferum in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KA2
- Type
- protein
- Length
- 598 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
- D4R
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thebaine synthase 2 (EC 4.2.99.24) | protein | 151 | 24% helix, 48% strand | A0A2U9GGW3 |
| B | Thebaine synthase 2 (EC 4.2.99.24) | protein | 152 | 26% helix, 47% strand | A0A2U9GGW3 |
| C | Thebaine synthase 2 (EC 4.2.99.24) | protein | 150 | 25% helix, 48% strand | A0A2U9GGW3 |
| D | Thebaine synthase 2 (EC 4.2.99.24) | protein | 145 | 23% helix, 44% strand | A0A2U9GGW3 |
Ligands and binding sites
- D4R · (4R,7aR,12bS)-7,9-dimethoxy-3-methyl-2,4,7a,13-tetrahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline · ligand · 3 copies · chains A, B, C
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 | 228 | 0.85 | 0.97 | 30 | D4R |
| 2 | 197 | 0.84 | 0.98 | 28 | D4R |
| 3 | 182 | 0.84 | 0.98 | 30 | D4R |
| 4 | 150 | 0.81 | 0.97 | 24 | empty |
| 5 | 963 | 0.80 | 0.82 | 95 | empty |
Interfaces
5 interfaces between chains.
- C–D · 927 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 233 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 80 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KA2 · Crystal structure of a Thebaine synthase from Papaver somniferum in complex with TBN · 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 6KA2 · PDBe 6KA2 · UniProt A0A2U9GGW3
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