Research workbench
X-ray structure of a cu-bound de novo designed peptide trimer
Analyse X-ray structure of a cu-bound de novo designed peptide trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L33
- Type
- protein
- Length
- 90 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cu-3SCC
- Ligands
- ACE, CU, NH2
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cu-3SCC | protein | 30 | 90% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, B, C
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
- NH2 · Amino group · ion · 2 copies · chains A, C
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 | 342 | 0.56 | 0.75 | 26 | empty |
| 2 | 112 | 0.43 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 212 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 167 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 163 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7L33 · X-ray Structure of a Cu-Bound De Novo Designed Peptide Trimer · 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 7L33 · PDBe 7L33
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