MolNFT v1 · #139851 · protein
Structure of coxsackievirus A6 (CVA6) virus a-particle in complex with the neutralizing antibody fragment 1D5
5XS7 · Light chain of Fab 1D5: “Structure of coxsackievirus A6 (CVA6) virus a-particle in complex with the neutralizing antibody fragment 1D5”. Electron microscopy, 10 pockets (best druggability 0.73). MolNFT v1 #139851 on GenesisL1: 3D…
- PDB
- 5XS7
- Type
- protein
- Length
- 861 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab 1D5; Heavy chain of Fab 1D5; Genome polyprotein
- UniProt
- A0A0K2BNC7
- Pockets
- 10 · best druggability 0.73
Structure
electron microscopy · 5 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain of Fab 1D5 | protein | 108 | 3% helix, 45% strand | — |
| H | Heavy chain of Fab 1D5 | protein | 119 | 3% helix, 49% strand | — |
| A | Genome polyprotein | protein | 214 | 9% helix, 27% strand | A0A0K2BNC7 |
| B | Genome polyprotein | protein | 205 | 12% helix, 33% strand | A0A0K2BNC7 |
| C | Genome polyprotein | protein | 215 | 8% helix, 33% strand | A0A0K2BNC7 |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.73 | 0.86 | 44 | empty |
| 2 | 81 | 0.49 | 0.83 | 22 | empty |
| 3 | 59 | 0.47 | 0.84 | 21 | empty |
| 4 | 100 | 0.47 | 0.80 | 21 | empty |
| 5 | 157 | 0.43 | 0.74 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2714 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1628 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1566 Ų buried · 7 hydrogen bonds · protein-protein
- L–H · 887 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 428 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5XS7 · Structure of Coxsackievirus A6 (CVA6) virus A-particle in complex with the neutralizing… · 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 A0A0K2BNC7
- Elsewhere: RCSB PDB 5XS7 · PDBe 5XS7 · UniProt A0A0K2BNC7
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