MolNFT v1 · #142646 · protein
MDM2 in complex with a D amino acid containing stapled peptide
6AAW · E3 ubiquitin-protein ligase MDM2: “MDM2 in complex with a D amino acid containing stapled peptide”. X-ray diffraction, 4 ligands (ACE, 0EH, 2JH). MolNFT v1 #142646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AAW
- Type
- protein
- Length
- 98 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; ACE-leu-thr-phe-stq-glu-tyr-dtr-gln-leu-cba-MK8-ser-ala…
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- ACE, 0EH, 2JH, NME
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 86 | 44% helix, 19% strand | Q00987 |
| B | ACE-leu-thr-phe-stq-glu-tyr-dtr-gln-leu-cba-MK8-ser-ala- ala | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- 0EH · (2R)-2-amino-2-methylnonanoic acid · ligand · chains A, B
- 2JH · 3-cyclobutyl-L-alanine · ligand · chains A, B
- NME · Methylamine · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 1 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 6AAW · Mdm2 in complex with a D amino Acid Containing 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 6AAW · PDBe 6AAW · UniProt Q00987
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