MolNFT v1 · #67792 · protein
Crystal structure of human MDM2 in complex with a potent miniature protein inhibitor (18-residues)
3IUX · E3 ubiquitin-protein ligase MDM2: “Crystal structure of human MDM2 in complex with a potent miniature protein inhibitor (18-residues)”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.62). MolNFT v1 #67792 on…
- PDB
- 3IUX
- Type
- protein
- Length
- 201 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Miniature protein inhibitor
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- CL
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 83 | 49% helix, 16% strand | Q00987 |
| B, D | Miniature protein inhibitor | protein | 18 | 44% helix, 0% strand | — |
| C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 82 | 46% helix, 13% strand | Q00987 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, C
- ACT · Acetate ion · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.62 | 0.79 | 37 | ACT |
| 2 | 79 | 0.38 | 0.78 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–B · 609 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 575 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 357 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 146 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 3IUX · Crystal structure of human MDM2 in complex with a potent miniature protein 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 3IUX · PDBe 3IUX · UniProt Q00987
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