MolNFT v1 · #47700 · protein
Crystal structure of human calcineurin in complex with pvivit peptide
2P6B · Pvivit 14-mer peptide: “Crystal structure of human calcineurin in complex with pvivit peptide”. X-ray diffraction, 5 ligands (CA, ZN, FE), 10 pockets (best druggability 0.68). MolNFT v1 #47700 on GenesisL1: 3D structure, binding…
- PDB
- 2P6B
- Type
- protein
- Length
- 1,026 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pvivit 14-mer peptide; Calmodulin-dependent calcineurin a subunit alpha isoform…
- UniProt
- Q08209, P63098
- Ligands
- CA, ZN, FE, PO4, NH2
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Pvivit 14-mer peptide | protein | 13 | 0% helix, 38% strand | — |
| A, C | Calmodulin-dependent calcineurin a subunit alpha isoform | protein | 357 | 36% helix, 17% strand | Q08209 |
| B | Calcineurin subunit B isoform 1 | protein | 146 | 56% helix, 5% strand | P63098 |
| D | Calcineurin subunit B isoform 1 | protein | 153 | 56% helix, 5% strand | P63098 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains B, D
- ZN · Zinc ion · metal · 2 copies · chains A, C
- FE · Fe (III) ion · metal · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
- NH2 · Amino group · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.68 | 0.95 | 18 | empty |
| 2 | 143 | 0.65 | 0.87 | 30 | empty |
| 3 | 61 | 0.50 | 0.86 | 22 | empty |
| 4 | 81 | 0.46 | 0.81 | 25 | empty |
| 5 | 116 | 0.46 | 0.78 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2113 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1931 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 747 Ų buried · 18 hydrogen bonds · protein-protein
- E–C · 463 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2P6B · Crystal Structure of Human Calcineurin in Complex with PVIVIT Peptide · the same entry in another collection · chain D against D, TM-score 1.00
- P63098 · AlphaFold monomer V2.0 prediction for calcineurin subunit B type 1 (P63098) · a predicted model of the same protein · chain D against A, TM-score 0.98
- 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
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
- Elsewhere: RCSB PDB 2P6B · PDBe 2P6B · UniProt Q08209 · UniProt P63098
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