MolNFT v1 · #187853 · protein
Hendra virus G protein head domain in complex with cross-neutralizing murine antibody HAH1.3
7SYZ · Attachment glycoprotein: “Hendra virus G protein head domain in complex with cross-neutralizing murine antibody HAH1.3”. X-ray diffraction, 5 ligands (NAG, FUC, BMA), 8 pockets (best druggability 0.65). MolNFT v1 #187853 on…
- PDB
- 7SYZ
- Type
- protein
- Length
- 858 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Attachment glycoprotein; Antibody HAH1.3 heavy chain; Antibody HAH1.3 light chain
- UniProt
- F4YH71
- Ligands
- NAG, FUC, BMA, MAN, SO4
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Attachment glycoprotein | protein | 416 | 3% helix, 48% strand | F4YH71 |
| H | Antibody HAH1.3 heavy chain | protein | 223 | 10% helix, 50% strand | — |
| L | Antibody HAH1.3 light chain | protein | 219 | 6% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, L
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains H, A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains L
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, H, L
- SO4 · Sulfate ion · ion · 15 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.65 | 0.78 | 45 | empty |
| 2 | 494 | 0.65 | 0.77 | 46 | empty |
| 3 | 151 | 0.59 | 0.83 | 29 | empty |
| 4 | 448 | 0.57 | 0.74 | 53 | empty |
| 5 | 77 | 0.50 | 0.84 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2068 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 579 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 335 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7SYZ · Hendra virus G protein head domain in complex with cross-neutralizing murine antibody… · 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 F4YH71
- Elsewhere: RCSB PDB 7SYZ · PDBe 7SYZ · UniProt F4YH71
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