Research workbench
X-ray structure of the human mitochondrial PRELID1 in complex with TRIAP1
Analyse X-ray structure of the human mitochondrial PRELID1 in complex with TRIAP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I3V
- Type
- protein
- Length
- 493 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
- MYR, NA, CL
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Preli domain-containing protein 1, mitochondrial | protein | 182 | 31% helix, 40% strand | Q9Y255 |
| B | Preli domain-containing protein 1, mitochondrial | protein | 173 | 33% helix, 39% strand | Q9Y255 |
| A, C | TP53-regulated inhibitor of apoptosis 1 | protein | 69 | 62% helix, 0% strand | O43715 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains F, B
- NA · Sodium ion · metal · 3 copies · chains B
- CL · Chloride ion · ion · 13 copies · chains F, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.58 | 0.76 | 48 | MYR, CL |
| 2 | 297 | 0.55 | 0.75 | 38 | MYR |
| 3 | 82 | 0.49 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1446 Ų buried · 18 hydrogen bonds · protein-protein
- F–A · 1428 Ų buried · 16 hydrogen bonds · protein-protein
- F–B · 381 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6I3V · x-ray structure of the human mitochondrial PRELID1 in complex with TRIAP1 · the same entry in another collection · chain F against F, 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 A against A, TM-score 0.96
- Q9Y255 · AlphaFold monomer V2.0 prediction for preli domain-containing protein 1, mitochondrial… · a predicted model of the same protein · chain B 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 6I3V · PDBe 6I3V · UniProt Q9Y255 · UniProt O43715
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