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Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor
Analyse Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TPX
- Type
- protein
- Length
- 284 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; D-peptide inhibitor dpmi-delta
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- CL, SO4
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 84 | 44% helix, 13% strand | Q00987 |
| B, D, F | D-peptide inhibitor dpmi-delta | protein | 11 | 64% helix, 0% strand | — |
| C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 83 | 45% helix, 18% strand | Q00987 |
| E | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 84 | 46% helix, 13% strand | Q00987 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains C, D, B, E
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, E, F
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.50 | 0.75 | 36 | CL |
| 2 | 96 | 0.38 | 0.76 | 19 | ACT |
Interfaces
8 interfaces between chains.
- A–C · 695 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 661 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 650 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 619 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 329 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 d-amino, 3 modified (D-amino acid, nonstandard).
Compared structures
- 3TPX · Crystal structure of human MDM2 in complex with a trifluoromethylated D-peptide inhibitor · 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 3TPX · PDBe 3TPX · UniProt Q00987
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