Research workbench
The structure of the copi coat linkage IV
Analyse The structure of the copi coat linkage IV in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A1Y
- Type
- protein
- Length
- 9,993 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor 1; Coatomer subunit alpha; Coatomer subunit beta'; Coatomer…
- UniProt
- P11076, Q8CIE6, O55029, Q9QZE5, P61924, Q9JIF7, Q5XJY5, O89079
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, I, J, R | ADP-ribosylation factor 1 | protein | 159 | 33% helix, 26% strand | P11076 |
| C, K | Coatomer subunit alpha | protein | 1126 | 26% helix, 24% strand | Q8CIE6 |
| D, L | Coatomer subunit beta' | protein | 803 | 19% helix, 35% strand | O55029 |
| E, V | Coatomer subunit gamma-1 | protein | 824 | 51% helix, 16% strand | Q9QZE5 |
| F, N, W | Coatomer subunit zeta-1 | protein | 139 | 42% helix, 23% strand | P61924 |
| G, O | Coatomer subunit beta | protein | 813 | 41% helix, 9% strand | Q9JIF7 |
| H | Coatomer subunit delta | protein | 380 | 14% helix, 43% strand | Q5XJY5 |
| M | Coatomer subunit gamma-1 | protein | 550 | 67% helix, 1% strand | Q9QZE5 |
| P | Coatomer subunit delta | protein | 135 | 41% helix, 26% strand | Q5XJY5 |
| X, Z | Coatomer subunit epsilon | protein | 292 | 78% helix, 0% strand | O89079 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.82 | 0.84 | 149 | empty |
| 2 | 976 | 0.80 | 0.83 | 148 | empty |
| 3 | 788 | 0.77 | 0.82 | 131 | empty |
| 4 | 778 | 0.76 | 0.81 | 111 | empty |
| 5 | 1049 | 0.76 | 0.79 | 131 | empty |
Interfaces
24 interfaces between chains.
- K–L · 906 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 901 Ų buried · 13 hydrogen bonds · protein-protein
- M–O · 688 Ų buried · 5 hydrogen bonds · protein-protein
- E–G · 686 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 530 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5A1Y · The structure of the COPI coat linkage IV · the same entry in another collection · chain I against I, 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 P11076
- Every structure of UniProt Q8CIE6
- Every structure of UniProt O55029
- Every structure of UniProt Q9QZE5
- Every structure of UniProt P61924
- Every structure of UniProt Q9JIF7
- Every structure of UniProt Q5XJY5
- Every structure of UniProt O89079
- Elsewhere: RCSB PDB 5A1Y · PDBe 5A1Y · UniProt P11076 · UniProt Q8CIE6 · UniProt O55029 · UniProt Q9QZE5 · UniProt P61924 · UniProt Q9JIF7 · UniProt Q5XJY5 · UniProt O89079
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