MolNFT v2 · #212888 · protein
Small peptide enhances the binding of nutline-3a to N-terminal domain of MdmX
8IA5 · Protein Mdm4: “Small peptide enhances the binding of nutline-3a to N-terminal domain of MdmX”. X-ray diffraction at 1.93, 2 ligands (NUT, O4B), 1 pocket (best druggability 0.60). MolNFT v2 #212888 on GenesisL1: 3D structure, binding…
- PDB
- 8IA5
- Type
- protein
- Length
- 95 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.93
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Protein Mdm4; 9-mer peptide
- UniProt
- O15151
- Ligands
- NUT, O4B
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · resolution 1.93 · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein Mdm4 | protein | 86 | 45% helix, 17% strand | O15151 |
| B | 9-mer peptide | protein | 9 | 56% helix, 0% strand | — |
Ligands and binding sites
- NUT · 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one · ligand · chains A, B
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.60 | 0.81 | 20 | NUT |
Interfaces
1 interface between chains.
- A–B · 349 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- O15151 · AlphaFold monomer V2.0 prediction for protein MDM4 (O15151) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O15151
- Elsewhere: RCSB PDB 8IA5 · PDBe 8IA5 · UniProt O15151
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