Research workbench
Het-N2 - de novo designed three-helix heterodimer with cysteine at the N2 position of the alpha-helix
Analyse Het-N2 - de novo designed three-helix heterodimer with cysteine at the N2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z0L
- Type
- protein
- Length
- 384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Positive strand; Cys-N2 strand
- Ligands
- ACE, CD, NA, NH2
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Positive strand | protein | 48 | 83% helix, 0% strand | — |
| B, D, F, H | Cys-N2 strand | protein | 48 | 79% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CD · Cadmium ion · metal · 5 copies · chains A, B, G, H, C, E, F, D
- NA · Sodium ion · metal · chains D
- NH2 · Amino group · ion · 8 copies · chains A, B, H, C, D, F, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.46 | 0.78 | 22 | CD |
| 2 | 66 | 0.35 | 0.77 | 18 | empty |
| 3 | 65 | 0.32 | 0.75 | 13 | CD |
| 4 | 75 | 0.30 | 0.74 | 13 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1300 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1287 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 1275 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1267 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 639 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6Z0L · Het-N2 - De novo designed three-helix heterodimer with Cysteine at the N2 position of the… · 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 6Z0L · PDBe 6Z0L
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