Research workbench
Structure of MDM2-MDMX-UbcH5B-ubiquitin complex
Analyse Structure of MDM2-MDMX-UbcH5B-ubiquitin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MNJ
- Type
- protein
- Length
- 698 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.16
- Source
- Homo sapiens
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; Polyubiquitin-B; E3 ubiquitin-protein ligase Mdm2…
- EC
- 2.3.2.23, 2.3.2.24, 6.3.2.-
- UniProt
- P62837, P0CG47, Q00987, O15151
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.16 · 7 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24) | protein | 146 | 36% helix, 18% strand | P62837 |
| B | Polyubiquitin-B | protein | 75 | 20% helix, 32% strand | P0CG47 |
| C | E3 ubiquitin-protein ligase Mdm2 (EC 6.3.2.-) | protein | 63 | 24% helix, 27% strand | Q00987 |
| D | Protein Mdm4 | protein | 63 | 24% helix, 32% strand | O15151 |
| F | Polyubiquitin-B | protein | 76 | 24% helix, 34% strand | P0CG47 |
| G | E3 ubiquitin-protein ligase Mdm2 (EC 6.3.2.-) | protein | 65 | 25% helix, 26% strand | Q00987 |
| H | Protein Mdm4 | protein | 64 | 27% helix, 31% strand | O15151 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains C, D, G, H
- SO4 · Sulfate ion · ion · 2 copies · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.74 | 0.77 | 84 | empty |
| 2 | 206 | 0.64 | 0.84 | 32 | empty |
| 3 | 246 | 0.63 | 0.81 | 27 | empty |
| 4 | 142 | 0.49 | 0.78 | 16 | empty |
| 5 | 156 | 0.48 | 0.77 | 18 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1129 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1043 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 839 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 556 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 5MNJ · Structure of MDM2-mdmx-UBCH5B-ubiquitin complex · the same entry in another collection · chain H against H, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O15151 · AlphaFold monomer V2.0 prediction for protein MDM4 (O15151) · a predicted model of the same protein · chain D against A, TM-score 0.92
- P0CG47 · AlphaFold monomer V2.0 prediction for polyubiquitin-B (P0CG47) · a predicted model of the same protein · chain F against A, TM-score 0.91
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 P62837
- Every structure of UniProt P0CG47
- Every structure of UniProt Q00987
- Every structure of UniProt O15151
- Elsewhere: RCSB PDB 5MNJ · PDBe 5MNJ · UniProt P62837 · UniProt P0CG47 · UniProt Q00987 · UniProt O15151
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