Research workbench
Cryo-EM structures of two intermediates provide insight into adenovirus assembly and disassembly
Analyse Cryo-EM structures of two intermediates provide insight into adenovirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZIF
- Type
- protein
- Length
- 11,817 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hexon protein; Penton protein; Pix; Pviii
- UniProt
- P03278, O71096, Q64845, O92788
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 16% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Hexon protein | protein | 903 | 15% helix, 26% strand | P03278 |
| M | Penton protein | protein | 450 | 11% helix, 26% strand | O71096 |
| N, O, P, Q | Pix | protein | 107 | 36% helix, 0% strand | Q64845 |
| R | Pviii | protein | 103 | 27% helix, 5% strand | O92788 |
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 | 1178 | 0.89 | 0.90 | 149 | empty |
| 2 | 1072 | 0.86 | 0.87 | 121 | empty |
| 3 | 1190 | 0.85 | 0.86 | 135 | empty |
| 4 | 832 | 0.85 | 0.87 | 102 | empty |
| 5 | 360 | 0.82 | 0.91 | 65 | empty |
Interfaces
42 interfaces between chains.
- J–K · 9051 Ų buried · 150 hydrogen bonds · protein-protein
- A–B · 9043 Ų buried · 150 hydrogen bonds · protein-protein
- D–E · 9039 Ų buried · 150 hydrogen bonds · protein-protein
- G–H · 9030 Ų buried · 150 hydrogen bonds · protein-protein
- D–F · 9026 Ų buried · 143 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3ZIF · Cryo-EM structures of two intermediates provide insight into adenovirus assembly and… · the same entry in another collection · chain A against A, 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 P03278
- Every structure of UniProt O71096
- Every structure of UniProt Q64845
- Every structure of UniProt O92788
- Elsewhere: RCSB PDB 3ZIF · PDBe 3ZIF · UniProt P03278 · UniProt O71096 · UniProt Q64845 · UniProt O92788
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