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The structure of the copi coat linkage I

Analyse The structure of the copi coat linkage I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NZT
Type: protein
Length: 6,978 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coatomer subunit alpha; Coatomer subunit epsilon; Coatomer subunit beta; Coatomer subunit…
UniProt: Q8CIE6, O89079, Q9JIF7, O55029, Q5XJY5, P11076, Q9QZE5, P61924
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 11 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coatomer subunit alpha	protein	1126	26% helix, 21% strand	Q8CIE6
E	Coatomer subunit epsilon	protein	292	78% helix, 0% strand	O89079
B	Coatomer subunit beta	protein	800	57% helix, 9% strand	Q9JIF7
C	Coatomer subunit beta'	protein	843	23% helix, 33% strand	O55029
D, I	Coatomer subunit delta	protein	177	50% helix, 19% strand	Q5XJY5
F, R, M, J	ADP-ribosylation factor 1	protein	159	29% helix, 21% strand	P11076
G	Coatomer subunit gamma-1	protein	798	53% helix, 14% strand	Q9QZE5
Z, L	Coatomer subunit zeta-1	protein	139	40% helix, 19% strand	P61924
K	Coatomer subunit gamma-1	protein	560	45% helix, 20% strand	Q9QZE5
N	Coatomer subunit beta	protein	570	74% helix, 0% strand	Q9JIF7
H	Coatomer subunit beta'	protein	721	17% helix, 38% strand	O55029

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	824	0.79	0.83	126	empty
2	786	0.78	0.82	126	empty
3	890	0.71	0.77	123	empty
4	1189	0.68	0.74	157	empty
5	503	0.68	0.79	61	empty

Interfaces

17 interfaces between chains.

A–C · 1050 Å² buried · 41 hydrogen bonds · protein-protein
A–E · 361 Å² buried · 1 hydrogen bond · protein-protein
G–H · 226 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 181 Å² buried · 2 hydrogen bonds · protein-protein
K–M · 128 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5NZT · The structure of the COPI coat linkage I · the same entry in another collection · chain L against L, 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 Q8CIE6
Every structure of UniProt O89079
Every structure of UniProt Q9JIF7
Every structure of UniProt O55029
Every structure of UniProt Q5XJY5
Every structure of UniProt P11076
Every structure of UniProt Q9QZE5
Every structure of UniProt P61924
Elsewhere: RCSB PDB 5NZT · PDBe 5NZT · UniProt Q8CIE6 · UniProt O89079 · UniProt Q9JIF7 · UniProt O55029 · UniProt Q5XJY5 · UniProt P11076 · UniProt Q9QZE5 · UniProt P61924

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