Research workbench
Structure of a phospholipid trafficking complex, native
Analyse Structure of a phospholipid trafficking complex, native in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XHR
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein UPS1, mitochondrial; Mitochondrial distribution and morphology protein 35
- UniProt
- Q05776, O60200
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein UPS1, mitochondrial | protein | 170 | 25% helix, 41% strand | Q05776 |
| N | Mitochondrial distribution and morphology protein 35 | protein | 71 | 63% helix, 0% strand | O60200 |
| M | Mitochondrial distribution and morphology protein 35 | protein | 71 | 63% helix, 0% strand | O60200 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.86 | 0.92 | 61 | empty |
| 2 | 874 | 0.83 | 0.85 | 88 | empty |
| 3 | 86 | 0.55 | 0.85 | 16 | empty |
| 4 | 153 | 0.51 | 0.79 | 23 | empty |
| 5 | 107 | 0.49 | 0.80 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–N · 1420 Ų buried · 15 hydrogen bonds · protein-protein
- B–M · 1402 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 240 Ų buried · 0 hydrogen bonds · protein-protein
- N–B · 230 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4XHR · Structure of a phospholipid trafficking complex, native · the same entry in another collection · chain A against A, TM-score 1.00
- Q05776 · AlphaFold monomer V2.0 prediction for protein UPS1, mitochondrial (Q05776) · a predicted model of the same protein · chain A against A, TM-score 0.97
- O60200 · AlphaFold monomer V2.0 prediction for mitochondrial distribution and morphology protein… · a predicted model of the same protein · chain N against A, TM-score 0.86
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 Q05776
- Every structure of UniProt O60200
- Elsewhere: RCSB PDB 4XHR · PDBe 4XHR · UniProt Q05776 · UniProt O60200
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