Research workbench
Schmallenberg virus glycoprotein gc head domain in complex with scfv 1C11
Analyse Schmallenberg virus glycoprotein gc head domain in complex with scfv 1C11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H3T
- Type
- protein
- Length
- 924 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv 1C11 vh; Scfv 1C11 vl; Envelopment polyprotein
- UniProt
- H2AM12
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I | Scfv 1C11 vh | protein | 118 | 3% helix, 50% strand | — |
| L, M | Scfv 1C11 vl | protein | 113 | 3% helix, 50% strand | — |
| A | Envelopment polyprotein | protein | 230 | 65% helix, 0% strand | H2AM12 |
| B | Envelopment polyprotein | protein | 232 | 64% helix, 0% strand | H2AM12 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains H, A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.76 | 0.79 | 83 | empty |
| 2 | 499 | 0.67 | 0.78 | 55 | empty |
| 3 | 389 | 0.65 | 0.79 | 46 | empty |
| 4 | 153 | 0.45 | 0.76 | 24 | empty |
| 5 | 86 | 0.42 | 0.79 | 26 | empty |
Interfaces
11 interfaces between chains.
- H–L · 954 Ų buried · 13 hydrogen bonds · protein-protein
- I–M · 944 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 774 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 514 Ų buried · 10 hydrogen bonds · protein-protein
- I–B · 513 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6H3T · Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with scFv 1C11 · the same entry in another collection · chain H against H, 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 H2AM12
- Elsewhere: RCSB PDB 6H3T · PDBe 6H3T · UniProt H2AM12
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