MolNFT v1 · #188562 · protein
Nipah virus attachment (G) glycoprotein ectodomain in complex with NAH1.3 neutralizing antibody Fab fragment (local refinement of the stalk region)
7TY0 · Glycoprotein G: “Nipah virus attachment (G) glycoprotein ectodomain in complex with NAH1.3 neutralizing antibody Fab fragment…”. Electron microscopy, 3 ligands (NAG, FUC, BMA), 20 pockets (best druggability 0.71). MolNFT v1 #188562…
- 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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