Research workbench
The structure of the copi coat leaf in complex with the ARFGAP2 uncoating factor
Analyse The structure of the copi coat leaf in complex with the ARFGAP2 uncoating factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NZS
- Type
- protein
- Length
- 4,873 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coatomer subunit alpha; Coatomer subunit beta; Coatomer subunit beta'; Coatomer subunit…
- UniProt
- Q8CIE6, Q9JIF7, O55029, Q5XJY5, P11076, Q9QZE5, P61924, Q3MID3
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 9 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coatomer subunit alpha | protein | 813 | 15% helix, 27% strand | Q8CIE6 |
| B | Coatomer subunit beta | protein | 800 | 57% helix, 9% strand | Q9JIF7 |
| C | Coatomer subunit beta' | protein | 843 | 23% helix, 33% strand | O55029 |
| D | Coatomer subunit delta | protein | 177 | 50% helix, 19% strand | Q5XJY5 |
| F, R, M | 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 |
| P | ADP-ribosylation factor GTPase-activating protein 2 | protein | 127 | 54% helix, 9% strand | Q3MID3 |
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 | 811 | 0.78 | 0.83 | 122 | empty |
| 2 | 759 | 0.78 | 0.83 | 116 | empty |
| 3 | 1073 | 0.69 | 0.74 | 123 | empty |
| 4 | 800 | 0.66 | 0.75 | 68 | empty |
| 5 | 527 | 0.66 | 0.78 | 53 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1045 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 181 Ų buried · 2 hydrogen bonds · protein-protein
- G–R · 129 Ų buried · 8 hydrogen bonds · protein-protein
- K–M · 125 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 96 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5NZS · The structure of the COPI coat leaf in complex with the ArfGAP2 uncoating factor · the same entry in another collection · chain P against P, 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 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
- Every structure of UniProt Q3MID3
- Elsewhere: RCSB PDB 5NZS · PDBe 5NZS · UniProt Q8CIE6 · UniProt Q9JIF7 · UniProt O55029 · UniProt Q5XJY5 · UniProt P11076 · UniProt Q9QZE5 · UniProt P61924 · UniProt Q3MID3
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