MolNFT v1 · #183292 · protein
Structure of the hantaan virus gn glycoprotein ectodomain in complex with Fab htn-GN1
7NKS · Envelope polyprotein: “Structure of the hantaan virus gn glycoprotein ectodomain in complex with Fab htn-GN1”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 20 pockets (best druggability 0.70). MolNFT v1 #183292 on GenesisL1: 3D…
- PDB
- 7NKS
- Type
- protein
- Length
- 1,550 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope polyprotein; Fab htn-GN1 heavy chain; Fab htn-GN1 light chain
- UniProt
- A0A077D153
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope polyprotein | protein | 336 | 14% helix, 41% strand | A0A077D153 |
| C | Fab htn-GN1 heavy chain | protein | 221 | 3% helix, 48% strand | — |
| D | Fab htn-GN1 light chain | protein | 216 | 7% helix, 54% strand | — |
| H | Fab htn-GN1 heavy chain | protein | 220 | 3% helix, 48% strand | — |
| L | Fab htn-GN1 light chain | protein | 215 | 8% helix, 53% strand | — |
| A | Envelope polyprotein | protein | 342 | 12% helix, 40% strand | A0A077D153 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, C, H, A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GOL · Glycerol · additive · 3 copies · chains B, C, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.70 | 0.81 | 39 | GOL |
| 2 | 100 | 0.69 | 0.92 | 27 | NAG |
| 3 | 102 | 0.65 | 0.90 | 23 | empty |
| 4 | 157 | 0.61 | 0.84 | 23 | empty |
| 5 | 56 | 0.61 | 0.92 | 19 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1712 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 1668 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 703 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 647 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 594 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7NKS · Structure of the Hantaan virus Gn glycoprotein ectodomain in complex with Fab HTN-Gn1 · the same entry in another collection · chain B against B, 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 A0A077D153
- Elsewhere: RCSB PDB 7NKS · PDBe 7NKS · UniProt A0A077D153
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