MolNFT v1 · #127843 · protein
Structure of truncated norcoclaurine synthase from thalictrum flavum
5N8Q · S-norcoclaurine synthase: “Structure of truncated norcoclaurine synthase from thalictrum flavum”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #127843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N8Q
- Type
- protein
- Length
- 477 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-norcoclaurine synthase
- EC
- 4.2.1.78
- UniProt
- Q67A25
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 160 | 26% helix, 43% strand | Q67A25 |
| B | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 158 | 28% helix, 42% strand | Q67A25 |
| C | S-norcoclaurine synthase (EC 4.2.1.78) | protein | 159 | 29% helix, 43% strand | Q67A25 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.72 | 0.85 | 32 | empty |
| 2 | 246 | 0.72 | 0.86 | 33 | empty |
| 3 | 249 | 0.71 | 0.85 | 35 | empty |
| 4 | 527 | 0.69 | 0.79 | 64 | empty |
| 5 | 132 | 0.38 | 0.73 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 629 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 628 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5N8Q · Structure of truncated Norcoclaurine Synthase from Thalictrum flavum · 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 0.98
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 5N8Q · PDBe 5N8Q · UniProt Q67A25
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