Research workbench
Crystal structure of 5A scfv complexed with yfv-china se in postfusion state
Analyse Crystal structure of 5A scfv complexed with yfv-china se in postfusion state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IVZ
- Type
- protein
- Length
- 617 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein; Heavy chain of monoclonal antibody 5A; Light chain of monoclonal…
- UniProt
- Q89292
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein | protein | 391 | 9% helix, 52% strand | Q89292 |
| H | Heavy chain of monoclonal antibody 5A | protein | 120 | 0% helix, 54% strand | — |
| L | Light chain of monoclonal antibody 5A | protein | 106 | 3% helix, 48% strand | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.59 | 0.82 | 31 | empty |
| 2 | 186 | 0.59 | 0.82 | 36 | empty |
| 3 | 160 | 0.45 | 0.76 | 24 | empty |
| 4 | 78 | 0.34 | 0.75 | 18 | empty |
| 5 | 58 | 0.27 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 855 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 840 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 137 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6IVZ · Crystal structure of 5A ScFv complexed with YFV-China sE in postfusion state · 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 Q89292
- Elsewhere: RCSB PDB 6IVZ · PDBe 6IVZ · UniProt Q89292
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