Research workbench
Chalcone synthase from glycine max (L.) merr (soybean) complexed with naringenin
Analyse Chalcone synthase from glycine max (L.) merr (soybean) complexed with naringenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BUR
- Type
- protein
- Length
- 777 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chalcone synthase 1
- EC
- 2.3.1.74
- UniProt
- P24826
- Ligands
- NAR
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chalcone synthase 1 (EC 2.3.1.74) | protein | 388 | 42% helix, 24% strand | P24826 |
| B | Chalcone synthase 1 (EC 2.3.1.74) | protein | 389 | 43% helix, 23% strand | P24826 |
Ligands and binding sites
- NAR · Naringenin · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.78 | 0.98 | 23 | NAR |
| 2 | 93 | 0.76 | 0.97 | 23 | NAR |
| 3 | 216 | 0.62 | 0.81 | 32 | CIT |
| 4 | 217 | 0.60 | 0.80 | 32 | CIT |
| 5 | 50 | 0.47 | 0.86 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3174 Ų buried · 68 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard, oxidation).
Compared structures
- 7BUR · Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin · the same entry in another collection · chain A against A, TM-score 1.00
- P24826 · AlphaFold monomer V2.0 prediction for chalcone synthase 1 (P24826) · a predicted model of the same protein · 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 P24826
- Elsewhere: RCSB PDB 7BUR · PDBe 7BUR · UniProt P24826
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