MolNFT v1 · #140135 · protein
Sftsv gn with neutralizing antibody MAB4-5
5Y11 · Mab 4-5 heavy chain: “Sftsv gn with neutralizing antibody MAB4-5”. X-ray diffraction, 2 ligands (NAG, MAN), 6 pockets (best druggability 0.55). MolNFT v1 #140135 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y11
- Type
- protein
- Length
- 753 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mab 4-5 heavy chain; Mab 4-5 light chain; Membrane glycoprotein polyprotein
- UniProt
- A0A1L2DAC8
- Ligands
- NAG, MAN
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mab 4-5 heavy chain | protein | 219 | 7% helix, 52% strand | — |
| B | Mab 4-5 light chain | protein | 215 | 6% helix, 49% strand | — |
| C | Membrane glycoprotein polyprotein | protein | 319 | 23% helix, 30% strand | A0A1L2DAC8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C
- MAN · alpha-D-mannopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.55 | 0.74 | 52 | empty |
| 2 | 83 | 0.52 | 0.84 | 28 | empty |
| 3 | 58 | 0.51 | 0.87 | 18 | empty |
| 4 | 182 | 0.43 | 0.74 | 30 | empty |
| 5 | 170 | 0.42 | 0.74 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1783 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 632 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5Y11 · SFTSV GN with neutralizing antibody MAb4-5 · 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 A0A1L2DAC8
- Elsewhere: RCSB PDB 5Y11 · PDBe 5Y11 · UniProt A0A1L2DAC8
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