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Crystal structure of yeast ALPHA/BETAPRIME-cop subcomplex of the copi vesicular coat

Analyse Crystal structure of yeast ALPHA/BETAPRIME-cop subcomplex of the copi vesicular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MKQ
Type: protein
Length: 2,961 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coatomer beta'-subunit; Coatomer subunit alpha
UniProt: A6ZU46, P53622
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 28% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coatomer beta'-subunit	protein	811	23% helix, 38% strand	A6ZU46
B, D	Coatomer subunit alpha	protein	177	63% helix, 1% strand	P53622
C	Coatomer beta'-subunit	protein	811	23% helix, 39% strand	A6ZU46
E	Coatomer beta'-subunit	protein	810	22% helix, 37% strand	A6ZU46
F	Coatomer subunit alpha	protein	175	66% helix, 1% strand	P53622

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1136	0.84	0.85	98	empty
2	717	0.82	0.86	67	empty
3	1002	0.81	0.82	82	empty
4	630	0.80	0.85	55	empty
5	716	0.80	0.84	75	empty

Interfaces

6 interfaces between chains.

C–D · 2305 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2269 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2178 Å² buried · 21 hydrogen bonds · protein-protein
C–E · 288 Å² buried · 1 hydrogen bond · protein-protein
A–E · 252 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3MKQ · Crystal structure of yeast alpha/betaprime-COP subcomplex of the COPI vesicular coat · the same entry in another collection · chain F against F, TM-score 1.00
P53622 · AlphaFold monomer V2.0 prediction for coatomer subunit alpha (P53622) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 A6ZU46
Every structure of UniProt P53622
Elsewhere: RCSB PDB 3MKQ · PDBe 3MKQ · UniProt A6ZU46 · UniProt P53622

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