Research workbench
Structure of a phospholipid trafficking complex with substrate
Analyse Structure of a phospholipid trafficking complex with substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XIZ
- Type
- protein
- Length
- 480 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
- Ligands
- LPP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein UPS1, mitochondrial | protein | 170 | 25% helix, 42% strand | Q05776 |
| M, N | Mitochondrial distribution and morphology protein 35 | protein | 70 | 64% helix, 0% strand | O60200 |
Ligands and binding sites
- LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.84 | 0.90 | 62 | LPP |
| 2 | 1103 | 0.81 | 0.82 | 100 | LPP |
| 3 | 50 | 0.46 | 0.85 | 13 | empty |
| 4 | 84 | 0.45 | 0.81 | 22 | empty |
| 5 | 96 | 0.43 | 0.79 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–M · 1409 Ų buried · 16 hydrogen bonds · protein-protein
- A–N · 1393 Ų buried · 16 hydrogen bonds · protein-protein
- A–M · 251 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 240 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4XIZ · Structure of a phospholipid trafficking complex with substrate · 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 M against A, TM-score 0.87
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 4XIZ · PDBe 4XIZ · UniProt Q05776 · UniProt O60200
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