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Crystal structure of hendra virus attachment G glycoprotein
Analyse Crystal structure of hendra virus attachment G glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PD4
- Type
- protein
- Length
- 865 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Attachment glycoprotein
- UniProt
- F4YH71
- Ligands
- NAG, FUC, BMA, SO4
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Attachment glycoprotein | protein | 436 | 2% helix, 47% strand | F4YH71 |
| B | Attachment glycoprotein | protein | 429 | 3% helix, 48% strand | F4YH71 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.68 | 0.79 | 43 | SO4 |
| 2 | 436 | 0.66 | 0.78 | 48 | SO4 |
| 3 | 91 | 0.64 | 0.90 | 29 | empty |
| 4 | 75 | 0.61 | 0.90 | 28 | empty |
| 5 | 235 | 0.54 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 759 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6PD4 · Crystal Structure of Hendra Virus Attachment G Glycoprotein · 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 6PD4 · PDBe 6PD4 · UniProt F4YH71
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