Research workbench
The structure of the copi coat linkage II
Analyse The structure of the copi coat linkage II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A1W
- Type
- protein
- Length
- 3,816 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 7 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor 1 | protein | 159 | 33% helix, 26% strand | P11076 |
| C | Coatomer subunit alpha | protein | 813 | 15% helix, 31% strand | Q8CIE6 |
| D | Coatomer subunit beta' | protein | 803 | 19% helix, 35% strand | O55029 |
| E | Coatomer subunit gamma-1 | protein | 550 | 67% helix, 1% strand | Q9QZE5 |
| F | Coatomer subunit zeta-1 | protein | 139 | 42% helix, 23% strand | P61924 |
| G | Coatomer subunit beta | protein | 813 | 41% helix, 9% strand | Q9JIF7 |
| H | Coatomer subunit delta | protein | 380 | 14% helix, 43% strand | Q5XJY5 |
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 | 858 | 0.76 | 0.81 | 143 | empty |
| 2 | 704 | 0.76 | 0.82 | 142 | empty |
| 3 | 757 | 0.75 | 0.81 | 142 | empty |
| 4 | 753 | 0.73 | 0.80 | 123 | empty |
| 5 | 726 | 0.73 | 0.80 | 86 | empty |
Interfaces
8 interfaces between chains.
- C–D · 903 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 688 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 528 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 393 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 384 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A1W · The structure of the COPI coat linkage II · the same entry in another collection · chain H against H, TM-score 1.00
- P11076 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P11076) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P61924 · AlphaFold monomer V2.0 prediction for coatomer subunit zeta-1 (P61924) · a predicted model of the same protein · chain F against A, TM-score 0.89
- O55029 · AlphaFold monomer V2.0 prediction for coatomer subunit beta' (O55029) · a predicted model of the same protein · chain D against A, TM-score 0.86
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
- Elsewhere: RCSB PDB 5A1W · PDBe 5A1W · UniProt P11076 · UniProt Q8CIE6 · UniProt O55029 · UniProt Q9QZE5 · UniProt P61924 · UniProt Q9JIF7 · UniProt Q5XJY5
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