MolNFT v1 · #70540 · protein
Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-alpha)
3LNJ · E3 ubiquitin-protein ligase MDM2: “Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-alpha)”. X-ray diffraction, 2 ligands (SO4, CL), 1 pocket (best druggability 0.46). MolNFT v1 #70540 on GenesisL1: 3D…
- PDB
- 3LNJ
- Type
- protein
- Length
- 280 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; D-peptide inhibitor
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- SO4, CL
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 83 | 47% helix, 13% strand | Q00987 |
| B, D | D-peptide inhibitor | protein | 11 | 64% helix, 0% strand | — |
| F | D-peptide inhibitor | protein | 9 | 56% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B
- CL · Chloride ion · ion · chains A, C
- GOL · Glycerol · additive · chains E
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 | 195 | 0.46 | 0.74 | 26 | empty |
Interfaces
9 interfaces between chains.
- A–C · 661 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 609 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 605 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 598 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 319 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 31 d-amino (D-amino acid).
Compared structures
- 3LNJ · Crystal structure of human MDM2 in complex with D-peptide inhibitor (DPMI-alpha) · 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 3LNJ · PDBe 3LNJ · UniProt Q00987
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