Research workbench
Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with ps
Analyse Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with ps in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I3Y
- Type
- protein
- Length
- 497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Preli domain-containing protein 1, mitochondrial; TP53-regulated inhibitor of apoptosis 1
- UniProt
- Q9Y255, O43715
- Ligands
- P5S
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Preli domain-containing protein 1, mitochondrial | protein | 173 | 26% helix, 39% strand | Q9Y255 |
| F | Preli domain-containing protein 1, mitochondrial | protein | 182 | 27% helix, 41% strand | Q9Y255 |
| A | TP53-regulated inhibitor of apoptosis 1 | protein | 74 | 51% helix, 0% strand | O43715 |
| H | TP53-regulated inhibitor of apoptosis 1 | protein | 68 | 57% helix, 0% strand | O43715 |
Ligands and binding sites
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 2 copies · chains C, F
- LMT · Dodecyl-beta-D-maltoside · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 151 | 0.65 | 0.86 | 28 | empty |
| 2 | 375 | 0.60 | 0.76 | 40 | P5S |
| 3 | 321 | 0.55 | 0.75 | 37 | P5S |
| 4 | 77 | 0.49 | 0.84 | 20 | empty |
| 5 | 50 | 0.45 | 0.84 | 11 | empty |
Interfaces
3 interfaces between chains.
- F–A · 1534 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 1340 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 442 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6I3Y · Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with PS · the same entry in another collection · chain H against H, TM-score 1.00
- O43715 · AlphaFold monomer V2.0 prediction for TP53-regulated inhibitor of apoptosis 1 (O43715) · a predicted model of the same protein · chain H against A, TM-score 0.90
- Q9Y255 · AlphaFold monomer V2.0 prediction for preli domain-containing protein 1, mitochondrial… · a predicted model of the same protein · chain C against A, TM-score 0.77
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 Q9Y255
- Every structure of UniProt O43715
- Elsewhere: RCSB PDB 6I3Y · PDBe 6I3Y · UniProt Q9Y255 · UniProt O43715
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