Research workbench
Crystal structure of K8
Analyse Crystal structure of K8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F08
- Type
- protein
- Length
- 3,024 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chalcone synthase
- Ligands
- COA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F, L | Chalcone synthase | protein | 377 | 41% helix, 24% strand | — |
| H | Chalcone synthase | protein | 379 | 39% helix, 24% strand | — |
| J | Chalcone synthase | protein | 379 | 40% helix, 23% strand | — |
| N | Chalcone synthase | protein | 380 | 39% helix, 25% strand | — |
| P | Chalcone synthase | protein | 378 | 40% helix, 24% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains B, D, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.83 | 0.85 | 101 | COA |
| 2 | 883 | 0.81 | 0.83 | 96 | empty |
| 3 | 771 | 0.81 | 0.84 | 73 | empty |
| 4 | 1189 | 0.79 | 0.81 | 102 | empty |
| 5 | 450 | 0.75 | 0.84 | 52 | empty |
Interfaces
12 interfaces between chains.
- H–N · 2653 Ų buried · 55 hydrogen bonds · protein-protein
- B–J · 2532 Ų buried · 49 hydrogen bonds · protein-protein
- F–P · 2503 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 1040 Ų buried · 21 hydrogen bonds · protein-protein
- F–H · 691 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7F08 · Crystal Structure of K8 · the same entry in another collection · chain B against B, 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 7F08 · PDBe 7F08
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