Research workbench
A conformation of cyclosporin a in aqueous environment revealed by the X-ray structure of a cyclosporin-Fab complex
Analyse A conformation of cyclosporin a in aqueous environment revealed by the X-ray… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IKF
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa R45-45-11 Fab (light chain); IGG1-kappa R45-45-11 Fab (heavy chain)…
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa R45-45-11 Fab (light chain) | protein | 214 | 7% helix, 50% strand | — |
| H | IGG1-kappa R45-45-11 Fab (heavy chain) | protein | 228 | 8% helix, 54% strand | — |
| C | Cyclosporin a | protein | 11 | 0% helix, 9% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.60 | 0.75 | 56 | empty |
| 2 | 137 | 0.50 | 0.79 | 21 | empty |
| 3 | 107 | 0.40 | 0.76 | 21 | empty |
| 4 | 94 | 0.36 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1929 Ų buried · 15 hydrogen bonds · protein-protein
- H–C · 502 Ų buried · 6 hydrogen bonds · protein-protein
- L–C · 196 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide, 1 d-amino (nonstandard, disulfide, methylation, D-amino acid).
Compared structures
- 1IKF · A conformation of cyclosporin a in aqueous environment revealed by the X-ray structure of… · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 1IKF · PDBe 1IKF
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