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Clathrin with bound beta2 appendage of AP2

Analyse Clathrin with bound beta2 appendage of AP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YAI
Type: protein
Length: 4,344 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 9.2
Source: Homo sapiens; Sus scrofa
Molecule: Clathrin heavy chain; AP-2 complex subunit beta; Clathrin light chain
UniProt: C0MHR2, P63010, F1S398
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · resolution 9.2 · 14 distinct chains · 60% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Clathrin heavy chain	protein	726	37% helix, 23% strand	C0MHR2
F	AP-2 complex subunit beta	protein	233	19% helix, 41% strand	P63010
C	Clathrin heavy chain	protein	513	68% helix, 0% strand	C0MHR2
M	Clathrin heavy chain	protein	518	67% helix, 0% strand	C0MHR2
A	Clathrin heavy chain	protein	379	73% helix, 0% strand	C0MHR2
B	Clathrin heavy chain	protein	468	65% helix, 0% strand	C0MHR2
D	Clathrin light chain	protein	104	75% helix, 0% strand	F1S398
O	Clathrin light chain	protein	59	86% helix, 0% strand	F1S398
J	Clathrin heavy chain	protein	165	73% helix, 0% strand	C0MHR2
K	Clathrin heavy chain	protein	257	71% helix, 1% strand	C0MHR2
L	Clathrin heavy chain	protein	548	68% helix, 0% strand	C0MHR2
H	Clathrin heavy chain	protein	236	64% helix, 0% strand	C0MHR2
I	Clathrin light chain	protein	58	45% helix, 0% strand	F1S398
N	Clathrin light chain	protein	80	60% helix, 0% strand	F1S398

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	696	0.82	0.86	83	empty
2	788	0.82	0.84	70	empty
3	568	0.79	0.85	75	empty
4	460	0.79	0.86	57	empty
5	497	0.79	0.86	61	empty

Interfaces

23 interfaces between chains.

A–D · 1823 Å² buried · 13 hydrogen bonds · protein-protein
K–N · 1667 Å² buried · 16 hydrogen bonds · protein-protein
J–I · 1227 Å² buried · 20 hydrogen bonds · protein-protein
O–L · 886 Å² buried · 5 hydrogen bonds · protein-protein
M–L · 608 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6YAI · Clathrin with bound BETA2 appendage of AP2 · the same entry in another collection · chain O against O, TM-score 1.00

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 C0MHR2
Every structure of UniProt P63010
Every structure of UniProt F1S398
Elsewhere: RCSB PDB 6YAI · PDBe 6YAI · UniProt C0MHR2 · UniProt P63010 · UniProt F1S398

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