Research workbench
Crystal structure of cyclophilin D in complex with csa analogue, JW47.
Analyse Crystal structure of cyclophilin D in complex with csa analogue, JW47. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A0E
- Type
- protein
- Length
- 351 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase F, mitochondrial; JW47
- EC
- 5.2.1.8
- UniProt
- P30405
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase F, mitochondrial (EC 5.2.1.8) | protein | 165 | 14% helix, 33% strand | P30405 |
| B | Peptidyl-prolyl cis-trans isomerase F, mitochondrial (EC 5.2.1.8) | protein | 164 | 15% helix, 34% strand | P30405 |
| C, E | JW47 | protein | 11 | 0% helix, 9% strand | — |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.34 | 0.73 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 577 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 500 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 5A0E · Crystal structure of cyclophilin D in complex with CsA analogue, JW47. · the same entry in another collection · chain A against A, TM-score 1.00
- P30405 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase F… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P30405
- Elsewhere: RCSB PDB 5A0E · PDBe 5A0E · UniProt P30405
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