Research workbench
Structure of calcineurin in complex with NHE1 peptide
Analyse Structure of calcineurin in complex with NHE1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NUF
- Type
- protein
- Length
- 535 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase 2B catalytic subunit alpha isoform; Calcineurin…
- EC
- 3.1.3.16
- UniProt
- Q08209, P63098, P19634
- Ligands
- CA, FE, ZN, NA, PO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% 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 | 360 | 36% helix, 17% strand | Q08209 |
| B | Calcineurin subunit B type 1 | protein | 156 | 62% helix, 5% strand | P63098 |
| C | SODIUM/HYDROGEN exchanger 1 | protein | 19 | 0% helix, 26% strand | P19634 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B
- FE · Fe (III) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.55 | 0.90 | 14 | empty |
| 2 | 143 | 0.51 | 0.79 | 23 | empty |
| 3 | 79 | 0.38 | 0.77 | 21 | empty |
| 4 | 56 | 0.32 | 0.77 | 16 | empty |
| 5 | 65 | 0.32 | 0.75 | 20 | FE, PO4, PGE |
Interfaces
3 interfaces between chains.
- A–B · 2206 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 290 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6NUF · Structure of Calcineurin in complex with NHE1 peptide · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
- P63098 · AlphaFold monomer V2.0 prediction for calcineurin subunit B type 1 (P63098) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P19634 · AlphaFold monomer V2.0 prediction for SODIUM/HYDROGEN exchanger 1 (P19634) · a predicted model of the same protein · chain C against A, TM-score 0.24
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 P19634
- Elsewhere: RCSB PDB 6NUF · PDBe 6NUF · UniProt Q08209 · UniProt P63098 · UniProt P19634
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