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Human cyclophilin C in complex with cyclosporin a
Analyse Human cyclophilin C in complex with cyclosporin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ESL
- Type
- protein
- Length
- 1,152 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase C; Cyclosporin a
- EC
- 5.2.1.8
- UniProt
- P45877
- Ligands
- CA, ZN, SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Peptidyl-prolyl cis-trans isomerase C (EC 5.2.1.8) | protein | 181 | 13% helix, 38% strand | P45877 |
| I, J, K, L, M, N | Cyclosporin a | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.85 | 0.88 | 146 | empty |
| 2 | 513 | 0.83 | 0.90 | 99 | empty |
| 3 | 95 | 0.38 | 0.76 | 18 | SO4 |
| 4 | 83 | 0.36 | 0.76 | 15 | SO4 |
| 5 | 102 | 0.35 | 0.74 | 20 | SO4 |
Interfaces
24 interfaces between chains.
- A–B · 568 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 565 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 547 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 6 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 2ESL · Human Cyclophilin C in Complex with Cyclosporin A · the same entry in another collection · chain N against N, 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 P45877
- Elsewhere: RCSB PDB 2ESL · PDBe 2ESL · UniProt P45877
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