Research workbench
Crystal structure of UPS1-MDM35 complex
Analyse Crystal structure of UPS1-MDM35 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YTW
- Type
- protein
- Length
- 484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial distribution and morphology protein 35; Protein UPS1, mitochondrial
- UniProt
- O60200, Q05776
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial distribution and morphology protein 35 | protein | 75 | 61% helix, 0% strand | O60200 |
| B | Protein UPS1, mitochondrial | protein | 168 | 26% helix, 43% strand | Q05776 |
| C | Mitochondrial distribution and morphology protein 35 | protein | 72 | 64% helix, 0% strand | O60200 |
| D | Protein UPS1, mitochondrial | protein | 169 | 25% helix, 43% strand | Q05776 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.85 | 0.91 | 65 | empty |
| 2 | 533 | 0.84 | 0.90 | 61 | empty |
| 3 | 150 | 0.55 | 0.81 | 29 | empty |
| 4 | 80 | 0.46 | 0.82 | 19 | empty |
| 5 | 77 | 0.35 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2644 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1453 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1389 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4YTW · Crystal structure of Ups1-Mdm35 complex · the same entry in another collection · chain D against D, TM-score 1.00
- O60200 · AlphaFold monomer V2.0 prediction for mitochondrial distribution and morphology protein… · a predicted model of the same protein · chain C against A, TM-score 0.85
- Q05776 · AlphaFold monomer V2.0 prediction for protein UPS1, mitochondrial (Q05776) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 O60200
- Every structure of UniProt Q05776
- Elsewhere: RCSB PDB 4YTW · PDBe 4YTW · UniProt O60200 · UniProt Q05776
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