MolNFT v1 · #87428 · protein
Cryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E19
4C10 · EV19 5 C1-6 F1 C11: “Cryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E19”. Electron microscopy, 3 ligands (SPH, NA, CL), 20 pockets (best druggability 0.80). MolNFT v1 #87428 on GenesisL1: 3D…
- PDB
- 4C10
- Type
- protein
- Length
- 1,276 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EV19 5 C1-6 F1 C11; VP1; VP3; VP2; VP4
- UniProt
- A9X4C2
- Ligands
- SPH, NA, CL
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 4 | EV19 5 C1-6 F1 C11 | protein | 217 | 6% helix, 53% strand | — |
| 5 | EV19 5 C1-6 F1 C11 | protein | 220 | 10% helix, 50% strand | — |
| A | VP1 | protein | 296 | 14% helix, 27% strand | A9X4C2 |
| B | VP3 | protein | 244 | 14% helix, 38% strand | A9X4C2 |
| C | VP2 | protein | 242 | 12% helix, 31% strand | A9X4C2 |
| D | VP4 | protein | 57 | 12% helix, 16% strand | A9X4C2 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
- NA · Sodium ion · metal · 6 copies · chains A, C, D, B
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.80 | 0.88 | 58 | SPH |
| 2 | 1009 | 0.77 | 0.79 | 131 | empty |
| 3 | 895 | 0.76 | 0.79 | 90 | empty |
| 4 | 498 | 0.73 | 0.82 | 90 | empty |
| 5 | 231 | 0.71 | 0.86 | 38 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4063 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 2716 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 1745 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1551 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1158 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4C10 · Cryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E19 · the same entry in another collection · chain 4 against 4, 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 A9X4C2
- Elsewhere: RCSB PDB 4C10 · PDBe 4C10 · UniProt A9X4C2
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