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
- 5NZV
- Type
- protein
- Length
- 9,995 residues
- Chains
- 22
- 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 0.78
Structure
electron microscopy · 10 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Coatomer subunit alpha | protein | 1126 | 26% helix, 21% strand | Q8CIE6 |
| E, O | Coatomer subunit epsilon | protein | 292 | 78% helix, 0% strand | O89079 |
| B, I | Coatomer subunit beta | protein | 800 | 57% helix, 9% strand | Q9JIF7 |
| C, J | Coatomer subunit beta' | protein | 843 | 23% helix, 33% strand | O55029 |
| D | Coatomer subunit delta | protein | 427 | 26% helix, 39% strand | Q5XJY5 |
| F, R, M, P, T | 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, U, S | Coatomer subunit zeta-1 | protein | 139 | 40% helix, 19% strand | P61924 |
| K, Q | Coatomer subunit gamma-1 | protein | 560 | 45% helix, 20% strand | Q9QZE5 |
| N | Coatomer subunit delta | protein | 177 | 50% helix, 19% 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 | 850 | 0.78 | 0.82 | 127 | empty |
| 2 | 829 | 0.78 | 0.83 | 121 | empty |
| 3 | 806 | 0.78 | 0.83 | 121 | empty |
| 4 | 1081 | 0.75 | 0.79 | 160 | empty |
| 5 | 949 | 0.68 | 0.74 | 78 | empty |
Interfaces
22 interfaces between chains.
- A–C · 1049 Ų buried · 41 hydrogen bonds · protein-protein
- H–J · 1045 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 360 Ų buried · 1 hydrogen bond · protein-protein
- H–O · 360 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 183 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5NZV · The structure of the COPI coat linkage IV · 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 5NZV · PDBe 5NZV · UniProt Q8CIE6 · UniProt O89079 · UniProt Q9JIF7 · UniProt O55029 · UniProt Q5XJY5 · UniProt P11076 · UniProt Q9QZE5 · UniProt P61924
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