Research workbench
Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes
Analyse Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M63
- Type
- protein
- Length
- 1,401 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE protein phosphatase 2B catalytic subunit, alpha isoform; Calcineurin B…
- EC
- 3.1.3.16, 5.2.1.8
- UniProt
- Q08209, P63098, P62937
- Ligands
- CA, ZN, FE
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE protein phosphatase 2B catalytic subunit, alpha isoform (EC 3.1.3.16) | protein | 372 | 34% helix, 15% strand | Q08209 |
| B | Calcineurin B subunit isoform 1 | protein | 158 | 46% helix, 4% strand | P63098 |
| C, G | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 165 | 14% helix, 33% strand | P62937 |
| D, H | Cyclosporin a | protein | 11 | 0% helix, 9% strand | — |
| E | SERINE/THREONINE protein phosphatase 2B catalytic subunit, alpha isoform (EC 3.1.3.16) | protein | 359 | 33% helix, 18% strand | Q08209 |
| F | Calcineurin B subunit isoform 1 | protein | 160 | 48% helix, 5% strand | P63098 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains B, F
- ZN · Zinc ion · metal · 2 copies · chains A, E
- FE · Fe (III) ion · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.84 | 0.85 | 112 | empty |
| 2 | 572 | 0.73 | 0.80 | 68 | empty |
| 3 | 59 | 0.69 | 0.96 | 20 | empty |
| 4 | 441 | 0.65 | 0.78 | 55 | empty |
| 5 | 266 | 0.64 | 0.82 | 41 | empty |
Interfaces
20 interfaces between chains.
- E–F · 2330 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2227 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 577 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 536 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 525 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 1M63 · Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct… · the same entry in another collection · chain H against H, TM-score 1.00
- Q08209 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2B catalytic… · a predicted model of the same protein · chain E against A, TM-score 0.96
- P63098 · AlphaFold monomer V2.0 prediction for calcineurin subunit B type 1 (P63098) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 Q08209
- Every structure of UniProt P63098
- Every structure of UniProt P62937
- Elsewhere: RCSB PDB 1M63 · PDBe 1M63 · UniProt Q08209 · UniProt P63098 · UniProt P62937
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