Research workbench
Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state
Analyse Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IW2
- Type
- protein
- Length
- 3,684 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens; Yellow fever virus (strain 17D vaccine)
- Molecule
- Envelope protein E; Heavy chain of monoclonal antibody 5A; Light chain of monoclonal…
- UniProt
- P03314
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.9 · 6 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 386 | 8% helix, 51% strand | P03314 |
| B, E, H, K, N, Q | Heavy chain of monoclonal antibody 5A | protein | 120 | 3% helix, 53% strand | — |
| C, F, I, O, R | Light chain of monoclonal antibody 5A | protein | 107 | 3% helix, 50% strand | — |
| D, G | Envelope protein E | protein | 388 | 8% helix, 50% strand | P03314 |
| J, M, P | Envelope protein E | protein | 387 | 8% helix, 50% strand | P03314 |
| L | Light chain of monoclonal antibody 5A | protein | 106 | 3% helix, 50% strand | — |
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 | 905 | 0.70 | 0.76 | 83 | empty |
| 2 | 864 | 0.70 | 0.76 | 64 | empty |
| 3 | 885 | 0.69 | 0.75 | 80 | empty |
| 4 | 726 | 0.65 | 0.74 | 60 | empty |
| 5 | 697 | 0.65 | 0.75 | 58 | empty |
Interfaces
31 interfaces between chains.
- M–P · 1391 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1350 Ų buried · 11 hydrogen bonds · protein-protein
- G–J · 1299 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 901 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 896 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide (disulfide).
Compared structures
- 6IW2 · Crystal structure of 5A scfv in complex with yfv-17D se in prefusion 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 P03314
- Elsewhere: RCSB PDB 6IW2 · PDBe 6IW2 · UniProt P03314
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