MolNFT v1 · #114379 · protein
Crystal structure of human enterovirus D68 in complex with 3'SLN
5BNP · Capsid protein VP1: “Crystal structure of human enterovirus D68 in complex with 3'SLN”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 11 pockets (best druggability 0.71). MolNFT v1 #114379 on GenesisL1: 3D structure, binding sites…
- PDB
- 5BNP
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4
- UniProt
- Q68T42
- Ligands
- NAG, GAL, SIA
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 287 | 10% helix, 33% strand | Q68T42 |
| B | Capsid protein VP2 | protein | 237 | 13% helix, 38% strand | Q68T42 |
| C | Capsid protein VP3 | protein | 247 | 10% helix, 28% strand | Q68T42 |
| D | Capsid protein VP4 | protein | 39 | 18% helix, 8% strand | Q68T42 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, C
- GAL · beta-D-galactopyranose · sugar · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.71 | 0.86 | 40 | empty |
| 2 | 71 | 0.63 | 0.90 | 22 | empty |
| 3 | 73 | 0.59 | 0.89 | 24 | empty |
| 4 | 150 | 0.50 | 0.79 | 27 | empty |
| 5 | 201 | 0.50 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4703 Ų buried · 84 hydrogen bonds · protein-protein
- A–B · 2117 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1892 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1215 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5BNP · Crystal structure of human enterovirus D68 in complex with 3'SLN · 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 Q68T42
- Elsewhere: RCSB PDB 5BNP · PDBe 5BNP · UniProt Q68T42
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