Research workbench
Ternary complex of a calcineurin a fragment, calcineurin B, FKBP12 and the immunosuppressant drug FK506 (tacrolimus)
Analyse Ternary complex of a calcineurin a fragment, calcineurin B, FKBP12 and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TCO
- Type
- protein
- Length
- 628 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE phosphatase B2; FK506-binding protein
- EC
- 3.1.3.16, 5.2.1.8
- UniProt
- P48452, P63099, P62942
- Ligands
- MYR, FK5, CA, ZN, FE, PO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE phosphatase B2 (EC 3.1.3.16) | protein | 352 | 37% helix, 18% strand | P48452 |
| B | SERINE/THREONINE phosphatase B2 (EC 3.1.3.16) | protein | 169 | 51% helix, 4% strand | P63099 |
| C | FK506-binding protein (EC 5.2.1.8) | protein | 107 | 13% helix, 40% strand | P62942 |
Ligands and binding sites
- MYR · Myristic acid · ligand · chains B
- FK5 · 8-deethyl-8-[but-3-enyl]-ascomycin · ligand · chains A, B, C
- CA · Calcium ion · metal · 4 copies · chains B
- ZN · Zinc ion · metal · chains A
- FE · Fe (III) ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.80 | 0.82 | 63 | FK5 |
| 2 | 397 | 0.71 | 0.82 | 55 | ZN, FE, PO4 |
| 3 | 125 | 0.58 | 0.84 | 22 | empty |
| 4 | 110 | 0.44 | 0.78 | 24 | empty |
| 5 | 64 | 0.37 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1947 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 468 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 1TCO · Ternary complex of a calcineurin a fragment, calcineurin B, FKBP12 and the… · the same entry in another collection · chain A against A, TM-score 1.00
- P62942 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1A (P62942) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P48452 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2B catalytic… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P63099 · AlphaFold monomer V2.0 prediction for calcineurin subunit B type 1 (P63099) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P48452
- Every structure of UniProt P63099
- Every structure of UniProt P62942
- Elsewhere: RCSB PDB 1TCO · PDBe 1TCO · UniProt P48452 · UniProt P63099 · UniProt P62942
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