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Nipah virus attachment (G) glycoprotein ectodomain in complex with NAH1.3 neutralizing antibody Fab fragment (local refinement of the distal 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
- 7TXZ
- Type
- protein
- Length
- 1,464 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein G; NAH1.3 Fab heavy chain; NAH1.3 Fab light chain
- UniProt
- Q9IH62
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G | protein | 470 | 8% helix, 43% strand | Q9IH62 |
| B | Glycoprotein G | protein | 471 | 6% helix, 43% strand | Q9IH62 |
| E, H | NAH1.3 Fab heavy chain | protein | 117 | 8% helix, 56% strand | — |
| F | NAH1.3 Fab light chain | protein | 110 | 3% helix, 52% strand | — |
| L | NAH1.3 Fab light chain | protein | 111 | 0% helix, 51% strand | — |
| D, C | Glycoprotein G | protein | 34 | 38% helix, 21% strand | Q9IH62 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, E, D, B, H, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.80 | 0.81 | 87 | empty |
| 2 | 523 | 0.70 | 0.80 | 47 | empty |
| 3 | 473 | 0.68 | 0.79 | 40 | empty |
| 4 | 330 | 0.63 | 0.79 | 59 | empty |
| 5 | 273 | 0.60 | 0.79 | 39 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1433 Ų buried · 7 hydrogen bonds · protein-protein
- H–L · 755 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 734 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 642 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 7TXZ · 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
- Elsewhere: RCSB PDB 7TXZ · PDBe 7TXZ · UniProt Q9IH62
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