Research workbench
Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-omega)
Analyse Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-omega) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KJM
- Type
- protein
- Length
- 193 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; D-pmi-omega
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- CL
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 85 | 45% helix, 20% strand | Q00987 |
| B, D | D-pmi-omega | protein | 12 | 75% helix, 0% strand | — |
| C | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 84 | 44% helix, 13% strand | Q00987 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, D
- IPA · Isopropyl alcohol · additive · chains A, B
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 | 68 | 0.38 | 0.78 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 633 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 620 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 607 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 136 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 134 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 d-amino, 2 modified (D-amino acid, nonstandard).
Compared structures
- 7KJM · Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-omega) · 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 7KJM · PDBe 7KJM · UniProt Q00987
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