Research workbench
Hendra virus attachment glycoprotein
Analyse Hendra virus attachment glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X9M
- Type
- protein
- Length
- 1,671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G
- UniProt
- O89343
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G | protein | 419 | 3% helix, 47% strand | O89343 |
| B | Glycoprotein G | protein | 418 | 3% helix, 48% strand | O89343 |
| C, D | Glycoprotein G | protein | 417 | 3% helix, 48% strand | O89343 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.84 | 0.88 | 85 | empty |
| 2 | 492 | 0.80 | 0.87 | 59 | empty |
| 3 | 449 | 0.79 | 0.87 | 47 | empty |
| 4 | 213 | 0.77 | 0.91 | 42 | empty |
| 5 | 237 | 0.77 | 0.90 | 50 | empty |
Interfaces
5 interfaces between chains.
- A–C · 918 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 891 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 886 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 609 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 2X9M · Hendra virus attachment 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 O89343
- Elsewhere: RCSB PDB 2X9M · PDBe 2X9M · UniProt O89343
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