MolNFT v1 · #145429 · protein
Influenza B/BRISBANE hemagglutinin Fab CR9115 SD84H complex
6CNV: “Influenza B/BRISBANE hemagglutinin Fab CR9115 SD84H complex”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.62). MolNFT v1 #145429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CNV
- Type
- protein
- Length
- 1,035 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Envelope glycoprotein; SD84H; CR9114 light chain; CR9114 Fab heavy chain
- UniProt
- U3RVK6, G4WYG8, M1E1E4
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 346 | 8% helix, 34% strand | U3RVK6 |
| B | Envelope glycoprotein | protein | 150 | 53% helix, 9% strand | G4WYG8, M1E1E4 |
| C | SD84H | protein | 116 | 10% helix, 48% strand | — |
| L | CR9114 light chain | protein | 209 | 6% helix, 51% strand | — |
| H | CR9114 Fab heavy chain | protein | 214 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.62 | 0.85 | 38 | empty |
| 2 | 308 | 0.57 | 0.76 | 32 | empty |
| 3 | 260 | 0.50 | 0.75 | 33 | empty |
| 4 | 260 | 0.48 | 0.73 | 37 | empty |
| 5 | 115 | 0.44 | 0.78 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2632 Ų buried · 35 hydrogen bonds · protein-protein
- L–H · 1516 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 694 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 568 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 197 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6CNV · Influenza B/BRISBANE hemagglutinin Fab CR9115 SD84H complex · 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 U3RVK6
- Every structure of UniProt G4WYG8
- Every structure of UniProt M1E1E4
- Elsewhere: RCSB PDB 6CNV · PDBe 6CNV · UniProt U3RVK6 · UniProt G4WYG8 · UniProt M1E1E4
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