Research workbench
Crystal structure of cyclosorus parasiticus chalcone synthase 1 (CPCHS1) complex with naringenin and CoA
Analyse Crystal structure of cyclosorus parasiticus chalcone synthase 1 (CPCHS1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VF0
- Type
- protein
- Length
- 1,575 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chalcone synthase
- Ligands
- NAR, COA
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chalcone synthase | protein | 391 | 40% helix, 23% strand | — |
| B, C | Chalcone synthase | protein | 396 | 40% helix, 23% strand | — |
| D | Chalcone synthase | protein | 392 | 41% helix, 23% strand | — |
Ligands and binding sites
- NAR · Naringenin · ligand · 4 copies · chains A, D, B, C
- COA · Coenzyme A · ligand · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.80 | 0.81 | 110 | NAR |
| 2 | 323 | 0.76 | 0.87 | 46 | NAR, COA |
| 3 | 297 | 0.75 | 0.87 | 46 | NAR, COA |
| 4 | 330 | 0.75 | 0.86 | 48 | NAR, COA |
| 5 | 53 | 0.70 | 0.97 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–C · 3534 Ų buried · 69 hydrogen bonds · protein-protein
- A–D · 3519 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 106 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7VF0 · Crystal structure of Cyclosorus parasiticus chalcone synthase 1 (CpCHS1) complex with… · 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
- Elsewhere: RCSB PDB 7VF0 · PDBe 7VF0
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