Research workbench
Multiple genomic RNA-coat protein contacts play vital roles in the assembly of infectious enterovirus-E
Analyse Multiple genomic RNA-coat protein contacts play vital roles in the assembly of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6THD
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P12915
- Ligands
- MYR, SO4
- Pockets
- 12 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 278 | 13% helix, 32% strand | P12915 |
| 2 | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 240 | 14% helix, 38% strand | P12915 |
| 3 | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 242 | 11% helix, 30% strand | P12915 |
| 4 | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 52 | 13% helix, 13% strand | P12915 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains 1, 3, 4
- SO4 · Sulfate ion · ion · 2 copies · chains 1, 2
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.85 | 0.96 | 42 | MYR |
| 2 | 144 | 0.51 | 0.80 | 24 | empty |
| 3 | 159 | 0.47 | 0.77 | 28 | empty |
| 4 | 140 | 0.47 | 0.78 | 35 | empty |
| 5 | 171 | 0.46 | 0.76 | 32 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 4168 Ų buried · 78 hydrogen bonds · protein-protein
- 1–2 · 2092 Ų buried · 37 hydrogen bonds · protein-protein
- 1–4 · 1574 Ų buried · 34 hydrogen bonds · protein-protein
- 2–3 · 1525 Ų buried · 12 hydrogen bonds · protein-protein
- 3–4 · 987 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6THD · Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious… · the same entry in another collection · chain 3 against 3, 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 P12915
- Elsewhere: RCSB PDB 6THD · PDBe 6THD · UniProt P12915
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