MolNFT v1 · #109961 · protein
Crystal structure of the mzm-rep domains of mind bomb 1 in complex with JAGGED1 N-box peptide
4XI7 · E3 ubiquitin-protein ligase MIB1: “Crystal structure of the mzm-rep domains of mind bomb 1 in complex with JAGGED1 N-box peptide”. X-ray diffraction, 2 ligands (ZN, SO4), 2 pockets (best druggability 0.78). MolNFT v1 #109961 on…
- PDB
- 4XI7
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MIB1; Jagged 1 N-box peptide
- EC
- 6.3.2.-
- UniProt
- Q86YT6
- Ligands
- ZN, SO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MIB1 (EC 6.3.2.-) | protein | 362 | 15% helix, 36% strand | Q86YT6 |
| C | Jagged 1 N-box peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
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 | 983 | 0.78 | 0.80 | 80 | empty |
| 2 | 144 | 0.49 | 0.78 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–C · 367 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4XI7 · Crystal structure of the MZM-REP domains of Mind bomb 1 in complex with Jagged1 N-box… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86YT6 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MIB1 (Q86YT6) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 Q86YT6
- Elsewhere: RCSB PDB 4XI7 · PDBe 4XI7 · UniProt Q86YT6
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