Research workbench
Structure of enterovirus 71 in complex with nld-22
Analyse Structure of enterovirus 71 in complex with nld-22 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LQD
- Type
- protein
- Length
- 842 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
- B2ZUN0
- Ligands
- EQ9
- Pockets
- 16 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 8% helix, 28% 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 | 297 | 6% helix, 24% strand | B2ZUN0 |
| B | Capsid protein VP2 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 245 | 8% helix, 35% strand | B2ZUN0 |
| C | Capsid protein VP3 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 242 | 10% helix, 30% strand | B2ZUN0 |
| D | Capsid protein VP4 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 58 | 10% helix, 9% strand | B2ZUN0 |
Ligands and binding sites
- EQ9 · 1-(2-azanylpyridin-4-yl)-3-[5-[4-(5-methyl-1,2,4-oxadiazol-3-yl)phenoxy]pentyl]imidazolidin-2-one · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.81 | 0.87 | 60 | EQ9 |
| 2 | 173 | 0.55 | 0.81 | 24 | empty |
| 3 | 69 | 0.55 | 0.88 | 20 | empty |
| 4 | 139 | 0.50 | 0.79 | 22 | empty |
| 5 | 154 | 0.47 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4058 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2760 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1693 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1483 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1082 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6LQD · Structure of Enterovirus 71 in complex with NLD-22 · 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 B2ZUN0
- Elsewhere: RCSB PDB 6LQD · PDBe 6LQD · UniProt B2ZUN0
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