Research workbench
Crystal structure of MDM2 bound to a stapled peptide
Analyse Crystal structure of MDM2 bound to a stapled peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H22
- Type
- protein
- Length
- 207 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Stapled peptide
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- ACE, FL5, NH2
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 91 | 47% helix, 14% strand | Q00987 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 92 | 47% helix, 14% strand | Q00987 |
| C, D | Stapled peptide | protein | 12 | 50% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, A, D
- FL5 · 12-(dimethylamino)-3,10-diethyl-N,N,N-trimethyl-3,10-dihydrodibenzo[3,4:7,8]cycloocta[1,2-D:5,6-d']bis([1, 2,3]triazole)-5-aminium · ligand · 2 copies · chains A, C, B, D
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.40 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 624 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 602 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 151 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6H22 · Crystal structure of Mdm2 bound to a stapled peptide · 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 6H22 · PDBe 6H22 · UniProt Q00987
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