Research workbench
A hexameric de novo coiled-coil assembly: cc-TYPE2-(VAYD)4-Y3F- W19(BRPHE).
Analyse A hexameric de novo coiled-coil assembly: cc-TYPE2-(VAYD)4-Y3F- W19(BRPHE). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BO9
- Type
- protein
- Length
- 179 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cc-TYPE2-(VAYD)4-Y3F-W19(BRPHE)
- Ligands
- ACE, NH2
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Cc-TYPE2-(VAYD)4-Y3F-W19(BRPHE) | protein | 30 | 93% helix, 0% strand | — |
| E | Cc-TYPE2-(VAYD)4-Y3F-W19(BRPHE) | protein | 29 | 93% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains B, D, A, C, E
- NH2 · Amino group · ion · 2 copies · chains C, F
- GOL · Glycerol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.31 | 0.75 | 17 | empty |
Interfaces
15 interfaces between chains.
- C–F · 812 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 771 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 682 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 672 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified, 3 covalent (nonstandard, covalent ligand).
Compared structures
- 7BO9 · A hexameric de novo coiled-coil assembly: CC-Type2-(VaYd)4-Y3F-W19(BrPhe). · 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 7BO9 · PDBe 7BO9
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