Research workbench
Human adenovirus type 3 fiber knob in complex with two copies of desmoglein-2
Analyse Human adenovirus type 3 fiber knob in complex with two copies of desmoglein-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QNU
- Type
- protein
- Length
- 920 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein; Desmoglein-2
- UniProt
- P04501, Q14126
- Pockets
- 11 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 2% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber protein | protein | 178 | 2% helix, 40% strand | P04501 |
| B | Fiber protein | protein | 181 | 4% helix, 38% strand | P04501 |
| C | Fiber protein | protein | 179 | 2% helix, 41% strand | P04501 |
| D | Desmoglein-2 | protein | 195 | 0% helix, 43% strand | Q14126 |
| E | Desmoglein-2 | protein | 187 | 2% helix, 42% strand | Q14126 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.82 | 0.88 | 43 | empty |
| 2 | 440 | 0.70 | 0.81 | 48 | empty |
| 3 | 587 | 0.70 | 0.78 | 60 | empty |
| 4 | 530 | 0.69 | 0.79 | 46 | empty |
| 5 | 60 | 0.69 | 0.96 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–B · 925 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 916 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 593 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6QNU · Human Adenovirus type 3 fiber knob in complex with two copies of Desmoglein-2 · the same entry in another collection · chain B against B, TM-score 1.00
- Q14126 · AlphaFold monomer V2.0 prediction for desmoglein-2 (Q14126) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P04501
- Every structure of UniProt Q14126
- Elsewhere: RCSB PDB 6QNU · PDBe 6QNU · UniProt P04501 · UniProt Q14126
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