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Nipah virus attachment (G) glycoprotein ectodomain in complex with NAH1.3 neutralizing antibody Fab fragment (local refinement of the stalk region)
Analyse Nipah virus attachment (G) glycoprotein ectodomain in complex with NAH1.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TY0
- Type
- protein
- Length
- 1,522 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G; Igh protein; Nah Fab light chain
- UniProt
- Q9IH62, I6L985
- Ligands
- NAG, FUC, BMA
- Pockets
- 20 · best druggability 0.71
Structure
electron microscopy · 8 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G | protein | 77 | 68% helix, 5% strand | Q9IH62 |
| B | Glycoprotein G | protein | 68 | 72% helix, 6% strand | Q9IH62 |
| J | Igh protein | protein | 103 | 9% helix, 53% strand | I6L985 |
| K | Igh protein | protein | 99 | 9% helix, 58% strand | I6L985 |
| N | Nah Fab light chain | protein | 105 | 6% helix, 48% strand | — |
| O | Nah Fab light chain | protein | 97 | 3% helix, 49% strand | — |
| D | Glycoprotein G | protein | 485 | 13% helix, 42% strand | Q9IH62 |
| C | Glycoprotein G | protein | 488 | 13% helix, 42% strand | Q9IH62 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, D, B, C, J
- FUC · alpha-L-fucopyranose · sugar · chains D
- BMA · beta-D-mannopyranose · sugar
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 | 380 | 0.71 | 0.82 | 51 | empty |
| 2 | 83 | 0.70 | 0.94 | 18 | empty |
| 3 | 321 | 0.68 | 0.83 | 50 | empty |
| 4 | 439 | 0.66 | 0.78 | 33 | empty |
| 5 | 82 | 0.65 | 0.92 | 27 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1589 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1571 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1038 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 972 Ų buried · 4 hydrogen bonds · protein-protein
- K–O · 711 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 7TY0 · Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing… · 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 Q9IH62
- Every structure of UniProt I6L985
- Elsewhere: RCSB PDB 7TY0 · PDBe 7TY0 · UniProt Q9IH62 · UniProt I6L985
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