Research workbench

AP2 clathrin adaptor core in active complex with cargo peptides

Analyse AP2 clathrin adaptor core in active complex with cargo peptides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XA7
Type: protein
Length: 1,768 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adaptor-related protein complex 2, alpha 2 subunit; Ap-2 complex subunit beta; Ap-2…
UniProt: Q66HM2, P63010, P84092, P62743
Ligands: SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adaptor-related protein complex 2, alpha 2 subunit	protein	613	71% helix, 1% strand	Q66HM2
B	Ap-2 complex subunit beta	protein	579	66% helix, 0% strand	P63010
M	Ap-2 complex subunit mu,	protein	428	16% helix, 38% strand	P84092
P	TGN38 cargo peptide	protein	6	0% helix, 33% strand	—
S	Ap-2 complex subunit sigma	protein	142	42% helix, 26% strand	P62743

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, S, B

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	90	0.76	0.97	21	empty
2	527	0.75	0.83	53	SO4
3	117	0.75	0.94	19	empty
4	448	0.74	0.83	45	empty
5	667	0.74	0.80	71	empty

Interfaces

7 interfaces between chains.

B–M · 4225 Å² buried · 51 hydrogen bonds · protein-protein
A–S · 2825 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 1971 Å² buried · 26 hydrogen bonds · protein-protein
M–P · 510 Å² buried · 6 hydrogen bonds · protein-protein
B–S · 310 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2XA7 · AP2 clathrin adaptor core in active complex with cargo peptides · the same entry in another collection · chain S against S, TM-score 1.00
P62743 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit sigma (P62743) · a predicted model of the same protein · chain S against A, TM-score 0.97
P84092 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit mu (P84092) · a predicted model of the same protein · chain M against A, TM-score 0.92
P63010 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit beta (P63010) · a predicted model of the same protein · chain B against A, TM-score 0.80

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 Q66HM2
Every structure of UniProt P63010
Every structure of UniProt P84092
Every structure of UniProt P62743
Elsewhere: RCSB PDB 2XA7 · PDBe 2XA7 · UniProt Q66HM2 · UniProt P63010 · UniProt P84092 · UniProt P62743

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