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Crystal structure of phosphatidic acid transporter UPS1/MDM35 void of bound phospholipid from saccharomyces cerevisiae at 1.5 ångströms resolution
Analyse Crystal structure of phosphatidic acid transporter UPS1/MDM35 void of bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JQM
- Type
- protein
- Length
- 706 residues
- Chains
- 3
- 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
- 7 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein UPS1, MITOCHONDRIAL,MITOCHONDRIAL distribution and morphology protein 35 | protein | 235 | 40% helix, 33% strand | Q05776, O60200 |
| B | Protein UPS1, MITOCHONDRIAL,MITOCHONDRIAL distribution and morphology protein 35 | protein | 235 | 37% helix, 33% strand | Q05776, O60200 |
| C | Protein UPS1, MITOCHONDRIAL,MITOCHONDRIAL distribution and morphology protein 35 | protein | 236 | 39% helix, 32% strand | Q05776, O60200 |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.90 | 0.91 | 117 | empty |
| 2 | 482 | 0.86 | 0.92 | 52 | empty |
| 3 | 455 | 0.85 | 0.92 | 54 | empty |
| 4 | 304 | 0.68 | 0.82 | 58 | empty |
| 5 | 98 | 0.52 | 0.83 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 811 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 749 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 727 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5JQM · Crystal Structure of Phosphatidic acid Transporter Ups1/Mdm35 Void of Bound Phospholipid… · 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 B against A, TM-score 0.70
- 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 0.29
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 5JQM · PDBe 5JQM · UniProt Q05776 · UniProt O60200
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