Research workbench
Macrocyclization of an all-D linear peptide improves target affinity and imparts cellular activity: a novel stapled alpha-helical peptide modality
Analyse Macrocyclization of an all-D linear peptide improves target affinity and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KZU
- Type
- protein
- Length
- 94 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; 2JN-dal-E03-dty-2JN-dsg-tdf-dgl-MK8-dle-dle-2JN
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- 2JN
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 85 | 46% helix, 22% strand | Q00987 |
| B | 2JN-dal-E03-dty-2JN-dsg-tdf-dgl-MK8-dle-dle-2JN | protein | 9 | 44% helix, 0% strand | — |
Ligands and binding sites
- 2JN · 2-methyl-D-norleucine · ligand · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 668 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 d-amino, 5 covalent, 3 modified (D-amino acid, covalent ligand, nonstandard).
Compared structures
- 6KZU · Macrocyclization of an all-D linear peptide improves target affinity and imparts cellular… · 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
- Every structure of UniProt Q00987
- Elsewhere: RCSB PDB 6KZU · PDBe 6KZU · UniProt Q00987
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