Research workbench
Structure of the stapled peptide bound to MDM2
Analyse Structure of the stapled peptide bound to MDM2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AFG
- Type
- protein
- Length
- 95 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Stapled peptide
- EC
- 6.3.2.19
- UniProt
- Q00987
- Ligands
- P07
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.19) | protein | 83 | 45% helix, 16% strand | Q00987 |
| B | Stapled peptide | protein | 12 | 75% helix, 0% strand | — |
Ligands and binding sites
- P07 · 1,8-diethyl-1,8-dihydrodibenzo[3,4:7,8][1,2,3]triazolo[4',5':5,6]cycloocta[1,2-d][1,2,3]triazole · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 5AFG · Structure of the Stapled Peptide Bound to Mdm2 · 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 5AFG · PDBe 5AFG · UniProt Q00987
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