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Crystal structure of rat cyclophilin D in complex with a potent nonimmunosuppressive inhibitor
Analyse Crystal structure of rat cyclophilin D in complex with a potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TOT
- Type
- protein
- Length
- 700 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase F, mitochondrial; Nonimmunosuppressive inhibitor
- EC
- 5.2.1.8
- UniProt
- P29117
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidyl-prolyl cis-trans isomerase F, mitochondrial (EC 5.2.1.8) | protein | 164 | 15% helix, 32% strand | P29117 |
| E, F, G, H | Nonimmunosuppressive inhibitor | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.46 | 0.77 | 25 | empty |
| 2 | 52 | 0.33 | 0.77 | 14 | empty |
| 3 | 56 | 0.26 | 0.73 | 21 | P6G |
Interfaces
10 interfaces between chains.
- D–H · 534 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 532 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 531 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 530 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 407 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 4 d-amino (nonstandard, D-amino acid, methylation).
Compared structures
- 4TOT · Crystal structure of rat cyclophilin D in complex with a potent nonimmunosuppressive… · the same entry in another collection · chain H against H, TM-score 1.00
- P29117 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase F… · a predicted model of the same protein · chain A 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 P29117
- Elsewhere: RCSB PDB 4TOT · PDBe 4TOT · UniProt P29117
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