Research workbench
Bacterial chalcone isomerase in closed conformation from eubacterium ramulus at 2.8 a resolution
Analyse Bacterial chalcone isomerase in closed conformation from eubacterium ramulus at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZPH
- Type
- protein
- Length
- 1,574 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chalcone isomerase
- EC
- 5.5.1.6
- Ligands
- CL
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chalcone isomerase (EC 5.5.1.6) | protein | 260 | 28% helix, 25% strand | — |
| B | Chalcone isomerase (EC 5.5.1.6) | protein | 282 | 30% helix, 24% strand | — |
| C, D, E, F | Chalcone isomerase (EC 5.5.1.6) | protein | 258 | 30% helix, 25% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, E
- GOL · Glycerol · additive · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.87 | 0.94 | 74 | empty |
| 2 | 515 | 0.86 | 0.93 | 72 | empty |
| 3 | 372 | 0.82 | 0.91 | 52 | empty |
| 4 | 355 | 0.81 | 0.90 | 47 | empty |
| 5 | 370 | 0.80 | 0.89 | 41 | empty |
Interfaces
12 interfaces between chains.
- A–E · 2226 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 2221 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 2205 Ų buried · 33 hydrogen bonds · protein-protein
- B–F · 1031 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 982 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3ZPH · Bacterial chalcone isomerase in closed conformation from Eubacterium ramulus at 2.8 A… · 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 3ZPH · PDBe 3ZPH
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