Research workbench
X-ray structure of a cypa-alisporivir complex at 1.5 ångström resolution
Analyse X-ray structure of a cypa-alisporivir complex at 1.5 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HSV
- Type
- protein
- Length
- 699 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase a; Alisporivir
- EC
- 5.2.1.8
- UniProt
- P62938
- Ligands
- CL
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 164 | 14% helix, 34% strand | P62938 |
| B | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 163 | 14% helix, 33% strand | P62938 |
| E, F, G, H | Alisporivir | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.67 | 0.74 | 80 | CL |
| 2 | 51 | 0.25 | 0.73 | 15 | empty |
Interfaces
8 interfaces between chains.
- D–H · 502 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 494 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 494 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 492 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 294 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 32 modified, 4 d-amino (nonstandard, D-amino acid, methylation).
Compared structures
- 5HSV · X-Ray structure of a CypA-Alisporivir complex at 1.5 angstrom resolution · the same entry in another collection · chain H against H, TM-score 1.00
- P62938 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase a (P62938) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P62938
- Elsewhere: RCSB PDB 5HSV · PDBe 5HSV · UniProt P62938
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