Research workbench
Het-ncap - de novo designed three-helix heterodimer with cysteine at the ncap position of the alpha-helix
Analyse Het-ncap - de novo designed three-helix heterodimer with cysteine at the ncap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z0M
- Type
- protein
- Length
- 384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Positive strand; Cys-ncap strand
- Ligands
- ACE, ZN, NH2, SO4
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Positive strand | protein | 48 | 88% helix, 0% strand | — |
| B, D, F, H | Cys-ncap strand | protein | 48 | 88% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · chains D, H
- NH2 · Amino group · ion · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.53 | 0.87 | 21 | empty |
| 2 | 60 | 0.26 | 0.72 | 18 | empty |
Interfaces
13 interfaces between chains.
- G–H · 1403 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1387 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1384 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1348 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 212 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6Z0M · Het-Ncap - De novo designed three-helix heterodimer with Cysteine at the Ncap position of… · the same entry in another collection · chain E against E, 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 6Z0M · PDBe 6Z0M
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