Research workbench
Rebuild and re-refined model for human parechovirus 1
Analyse Rebuild and re-refined model for human parechovirus 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MJV
- Type
- protein + RNA
- Length
- 694 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid subunit VP1; Capsid subunit VP3; Capsid subunit VP0; RNA…
- EC
- 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- Q66578
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid subunit VP1 (EC 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 192 | 13% helix, 38% strand | Q66578 |
| B | Capsid subunit VP3 (EC 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 239 | 9% helix, 33% strand | Q66578 |
| C | Capsid subunit VP0 (EC 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 257 | 13% helix, 33% strand | Q66578 |
| D | RNA (5'-R(*GP*UP*UP*UP*UP*U)-3') | rna | 6 | — | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.71 | 0.81 | 49 | empty |
| 2 | 117 | 0.44 | 0.78 | 27 | empty |
| 3 | 74 | 0.38 | 0.78 | 16 | empty |
| 4 | 64 | 0.36 | 0.78 | 19 | empty |
| 5 | 57 | 0.33 | 0.77 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3409 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 1254 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1123 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 291 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 148 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 5MJV · Rebuild and re-refined model for Human Parechovirus 1 · 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 Q66578
- Elsewhere: RCSB PDB 5MJV · PDBe 5MJV · UniProt Q66578
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