Research workbench

AP2 bound to heparin and TGN38 tyrosine cargo peptide

Analyse AP2 bound to heparin and TGN38 tyrosine cargo peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RWA
Type: protein
Length: 3,244 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ap-2 complex subunit alpha-2; Ap-2 complex subunit beta; Ap-2 complex subunit mu; Ap-2…
UniProt: P17427, Q9DBG3, P84091, P62743
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 5 distinct chains · 54% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, a	Ap-2 complex subunit alpha-2	protein	600	71% helix, 1% strand	P17427
B, b	Ap-2 complex subunit beta	protein	496	67% helix, 0% strand	Q9DBG3
M, m	Ap-2 complex subunit mu	protein	379	13% helix, 46% strand	P84091
S, s	Ap-2 complex subunit sigma	protein	142	46% helix, 25% strand	P62743
Y, y	Trans-golgi network integral membrane protein TGN38 peptide	protein	5	0% helix, 60% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1037	0.81	0.83	125	empty
2	1060	0.81	0.82	131	empty
3	779	0.79	0.83	125	empty
4	1105	0.78	0.80	98	empty
5	939	0.78	0.80	127	empty

Interfaces

12 interfaces between chains.

A–S · 493 Å² buried · 2 hydrogen bonds · protein-protein
a–s · 491 Å² buried · 2 hydrogen bonds · protein-protein
B–M · 369 Å² buried · 1 hydrogen bond · protein-protein
b–m · 367 Å² buried · 1 hydrogen bond · protein-protein
m–y · 350 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7RWA · AP2 bound to heparin and Tgn38 tyrosine cargo peptide · the same entry in another collection · chain y against y, 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 0.95

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 P17427
Every structure of UniProt Q9DBG3
Every structure of UniProt P84091
Every structure of UniProt P62743
Elsewhere: RCSB PDB 7RWA · PDBe 7RWA · UniProt P17427 · UniProt Q9DBG3 · UniProt P84091 · UniProt P62743

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