MolNFT v1 · #142711 · protein
The structure of CVA10 mature virion in complex with Fab 2G8
6AD0 · Vl of Fab 2G8: “The structure of CVA10 mature virion in complex with Fab 2G8”. Electron microscopy, 1 ligand (SPH), 17 pockets (best druggability 0.84). MolNFT v1 #142711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AD0
- Type
- protein
- Length
- 1,034 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vl of Fab 2G8; Vh of Fab 2G8; VP1; VP2; VP3; VP4
- UniProt
- A0A1V0FT21, Q75Q92
- Ligands
- SPH
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 6% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Vl of Fab 2G8 | protein | 111 | 0% helix, 25% strand | — |
| H | Vh of Fab 2G8 | protein | 114 | 3% helix, 29% strand | — |
| A | VP1 | protein | 285 | 7% helix, 26% strand | A0A1V0FT21 |
| B | VP2 | protein | 243 | 4% helix, 32% strand | A0A1V0FT21 |
| C | VP3 | protein | 240 | 9% helix, 27% strand | A0A1V0FT21 |
| D | VP4 | protein | 41 | 7% helix, 7% strand | Q75Q92 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.84 | 0.90 | 67 | SPH |
| 2 | 326 | 0.64 | 0.80 | 41 | empty |
| 3 | 325 | 0.62 | 0.79 | 43 | empty |
| 4 | 314 | 0.62 | 0.79 | 37 | empty |
| 5 | 78 | 0.61 | 0.90 | 25 | empty |
Interfaces
13 interfaces between chains.
- A–C · 3785 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2333 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1783 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1390 Ų buried · 15 hydrogen bonds · protein-protein
- L–H · 850 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6AD0 · The structure of CVA10 mature virion in complex with Fab 2G8 · the same entry in another collection · chain L against L, 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 A0A1V0FT21
- Every structure of UniProt Q75Q92
- Elsewhere: RCSB PDB 6AD0 · PDBe 6AD0 · UniProt A0A1V0FT21 · UniProt Q75Q92
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