Research workbench
Bacterial chalcone isomerase complexed with naringenin
Analyse Bacterial chalcone isomerase 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
- 4D06
- Type
- protein
- Length
- 1,623 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chalcone isomerase
- EC
- 5.5.1.6
- UniProt
- V9P0A9
- Ligands
- NAR, X8W, CL
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Chalcone isomerase (EC 5.5.1.6) | protein | 282 | 30% helix, 23% strand | V9P0A9 |
| B, D, F | Chalcone isomerase (EC 5.5.1.6) | protein | 259 | 31% helix, 24% strand | V9P0A9 |
Ligands and binding sites
- NAR · Naringenin · ligand · 7 copies · chains A, C, D, E, F
- X8W · (2E)-3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)prop-2-en-1-one · ligand · 2 copies · chains B, D
- CL · Chloride ion · ion · 17 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.90 | 0.93 | 130 | empty |
| 2 | 377 | 0.82 | 0.91 | 53 | empty |
| 3 | 392 | 0.82 | 0.90 | 52 | empty |
| 4 | 391 | 0.82 | 0.90 | 55 | empty |
| 5 | 92 | 0.77 | 0.97 | 26 | NAR |
Interfaces
12 interfaces between chains.
- C–D · 2208 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2204 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2202 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1021 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1017 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4D06 · Bacterial chalcone isomerase complexed with naringenin · 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 V9P0A9
- Elsewhere: RCSB PDB 4D06 · PDBe 4D06 · UniProt V9P0A9
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