MolNFT v1 · #169884 · protein
Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of A/AICHI/2/1968 (X-31)(H3N2)
6XPX: “Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of A/AICHI/2/1968 (X-31)(H3N2)”. X-ray diffraction, 3 ligands (BCN, NAG, BMA), 4 pockets (best druggability 0.57). MolNFT v1 #169884 on GenesisL1: 3D…
- PDB
- 6XPX
- Type
- protein
- Length
- 702 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; S1V2-51 Fab light chain; S1V2-51 Fab heavy chain
- UniProt
- P03437
- Ligands
- BCN, NAG, BMA
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 271 | 13% helix, 38% strand | P03437 |
| C | S1V2-51 Fab light chain | protein | 218 | 6% helix, 49% strand | — |
| B | S1V2-51 Fab heavy chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- BCN · Bicine · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 7 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.57 | 0.74 | 48 | empty |
| 2 | 280 | 0.50 | 0.74 | 45 | BCN, GOL |
| 3 | 116 | 0.37 | 0.74 | 26 | 1PE |
| 4 | 68 | 0.28 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1700 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, additive adduct).
Compared structures
- 6XPX · Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of… · 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 P03437
- Elsewhere: RCSB PDB 6XPX · PDBe 6XPX · UniProt P03437
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