Research workbench
X-ray structure of norcoclaurine synthase from thalictrum flavum in complex with dopamine and hydroxybenzaldehyde
Analyse X-ray structure of norcoclaurine synthase from thalictrum flavum in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VQ5
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-norcoclaurine synthase
- EC
- 4.2.1.78
- UniProt
- Q67A25
- Ligands
- HBA, LDP, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 173 | 27% helix, 40% strand | Q67A25 |
| B | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 155 | 28% helix, 41% strand | Q67A25 |
Ligands and binding sites
- HBA · P-hydroxybenzaldehyde · ligand · 2 copies · chains A, B
- LDP · L-dopamine · ligand · chains B
- CL · Chloride ion · ion · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.73 | 0.86 | 37 | LDP, HBA |
| 2 | 216 | 0.70 | 0.86 | 37 | HBA |
| 3 | 116 | 0.60 | 0.86 | 22 | CL |
| 4 | 106 | 0.38 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2VQ5 · X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q67A25 · AlphaFold monomer V2.0 prediction for S-norcoclaurine synthase (Q67A25) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q67A25
- Elsewhere: RCSB PDB 2VQ5 · PDBe 2VQ5 · UniProt Q67A25
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