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Cryo-EM structure of phosphorylated ap-2 (mu E302K) bound to necap in the presence of ss DNA

Analyse Cryo-EM structure of phosphorylated ap-2 (mu E302K) bound to necap in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OXL
Type: protein
Length: 1,815 residues
Chains: 6
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: Q9DBG3, P84091, P62744, Q9D1J1
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 6 distinct chains · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ap-2 complex subunit alpha-2	protein	589	69% helix, 1% strand	—
B	Ap-2 complex subunit beta	protein	564	63% helix, 0% strand	Q9DBG3
M	Ap-2 complex subunit mu	protein	390	12% helix, 43% strand	P84091
S	Ap-2 complex subunit sigma	protein	141	39% helix, 23% strand	P62744
N	Adaptin ear-binding coat-associated protein 2	protein	124	23% helix, 43% strand	Q9D1J1
n	Unknown region of adaptin ear-binding coat-associated protein 2 ex-domain	protein	7	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	995	0.85	0.86	104	empty
2	633	0.81	0.86	77	empty
3	789	0.80	0.83	65	empty
4	853	0.78	0.81	90	empty
5	280	0.73	0.87	37	empty

Interfaces

9 interfaces between chains.

B–M · 3359 Å² buried · 33 hydrogen bonds · protein-protein
A–S · 2566 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1742 Å² buried · 22 hydrogen bonds · protein-protein
A–M · 1067 Å² buried · 11 hydrogen bonds · protein-protein
M–N · 789 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

6OXL · CRYO-EM STRUCTURE OF PHOSPHORYLATED AP-2 (mu E302K) BOUND TO NECAP IN THE PRESENCE OF SS… · the same entry in another collection · chain n against n, TM-score 1.00
P62744 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit sigma (P62744) · a predicted model of the same protein · chain S against A, TM-score 0.98
Q9D1J1 · AlphaFold monomer V2.0 prediction for adaptin ear-binding coat- associated protein 2… · a predicted model of the same protein · chain N against A, TM-score 0.96
Q9DBG3 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit beta (Q9DBG3) · a predicted model of the same protein · chain B against A, TM-score 0.94
P84091 · AlphaFold monomer V2.0 prediction for ap-2 complex subunit mu (P84091) · a predicted model of the same protein · chain M against A, TM-score 0.61

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 Q9DBG3
Every structure of UniProt P84091
Every structure of UniProt P62744
Every structure of UniProt Q9D1J1
Elsewhere: RCSB PDB 6OXL · PDBe 6OXL · UniProt Q9DBG3 · UniProt P84091 · UniProt P62744 · UniProt Q9D1J1

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