MolNFT v1 · #125803 · protein
Structure of hantavirus envelope glycoprotein gc in complex with scfv A5
5LJY · Envelopment polyprotein: “Structure of hantavirus envelope glycoprotein gc in complex with scfv A5”. X-ray diffraction, 2 ligands (NCO, NAG), 5 pockets (best druggability 0.64). MolNFT v1 #125803 on GenesisL1: 3D structure, binding…
- PDB
- 5LJY
- Type
- protein
- Length
- 594 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelopment polyprotein; SCFVA5
- UniProt
- P08668
- Ligands
- NCO, NAG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelopment polyprotein | protein | 374 | 4% helix, 60% strand | P08668 |
| H | SCFVA5 | protein | 113 | 0% helix, 49% strand | — |
| L | SCFVA5 | protein | 107 | 7% helix, 48% strand | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.64 | 0.90 | 21 | empty |
| 2 | 81 | 0.42 | 0.79 | 18 | empty |
| 3 | 97 | 0.39 | 0.77 | 19 | empty |
| 4 | 54 | 0.35 | 0.79 | 15 | empty |
| 5 | 51 | 0.34 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 699 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 678 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 471 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5LJY · Structure of hantavirus envelope glycoprotein Gc in complex with scFv A5 · 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 P08668
- Elsewhere: RCSB PDB 5LJY · PDBe 5LJY · UniProt P08668
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