Research workbench
Coxsackievirus B3 in complex with capsid binder compound 17
Analyse Coxsackievirus B3 in complex with capsid binder compound 17 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZCL
- Type
- protein
- Length
- 813 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P03313
- Ligands
- FHK, MYR
- Pockets
- 9 · best druggability 0.66
Structure
electron microscopy · 4 distinct chains · 5% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 269 | 8% helix, 30% strand | P03313 |
| B | Capsid protein VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 252 | 4% helix, 37% strand | P03313 |
| C | Capsid protein VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 237 | 2% helix, 32% strand | P03313 |
| D | Capsid protein VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 55 | 5% helix, 16% strand | P03313 |
Ligands and binding sites
- FHK · 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid · ligand · chains A, C
- MYR · Myristic acid · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.66 | 0.87 | 34 | empty |
| 2 | 114 | 0.50 | 0.81 | 21 | empty |
| 3 | 71 | 0.48 | 0.84 | 19 | empty |
| 4 | 118 | 0.47 | 0.79 | 21 | empty |
| 5 | 124 | 0.44 | 0.77 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4281 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 2176 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1626 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1105 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 951 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 6ZCL · Coxsackievirus B3 in complex with capsid binder compound 17 · 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 P03313
- Elsewhere: RCSB PDB 6ZCL · PDBe 6ZCL · UniProt P03313
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