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Crystal structure of calcineurin in complex with AKAP79 peptide

Analyse Crystal structure of calcineurin in complex with AKAP79 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LL8
Type: protein
Length: 1,035 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AKAP79 peptide; SERINE/THREONINE-protein phosphatase 2B catalytic subunit alpha isoform…
EC: 3.1.3.16
UniProt: P24588, Q08209, P63098
Ligands: CA, ZN, FE, PO4
Pockets: 11 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	AKAP79 peptide	protein	11	0% helix, 55% strand	P24588
A, C	SERINE/THREONINE-protein phosphatase 2B catalytic subunit alpha isoform (EC 3.1.3.16)	protein	357	36% helix, 17% strand	Q08209
B, D	Calcineurin subunit B type 1	protein	155	62% helix, 3% 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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	811	0.79	0.82	79	PO4, FE
2	506	0.72	0.81	56	empty
3	255	0.70	0.85	41	empty
4	136	0.69	0.89	29	empty
5	245	0.68	0.84	48	empty

Interfaces

6 interfaces between chains.

A–B · 2140 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 2076 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1486 Å² buried · 5 hydrogen bonds · protein-protein
E–A · 679 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 277 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3LL8 · Crystal Structure of Calcineurin in Complex with AKAP79 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
P24588 · AlphaFold monomer V2.0 prediction for a-kinase anchor protein 5 (P24588) · a predicted model of the same protein · chain E against A, TM-score 0.41

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 P24588
Every structure of UniProt Q08209
Every structure of UniProt P63098
Elsewhere: RCSB PDB 3LL8 · PDBe 3LL8 · UniProt P24588 · UniProt Q08209 · UniProt P63098

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