Research workbench
Crystal structure of heterosubtypic Fab S139/1 in complex with influenza a H3 hemagglutinin
Analyse Crystal structure of heterosubtypic Fab S139/1 in complex with influenza a H3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GMS
- Type
- protein
- Length
- 2,657 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Fab S139/1 light chain; Fab S139/1…
- UniProt
- P03435
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 316 | 10% helix, 43% strand | P03435 |
| B, D, F | Hemagglutinin HA2 chain | protein | 171 | 52% helix, 15% strand | P03435 |
| L | Fab S139/1 light chain | protein | 211 | 7% helix, 50% strand | — |
| H | Fab S139/1 heavy chain | protein | 218 | 7% helix, 53% strand | — |
| M | Fab S139/1 light chain | protein | 156 | 2% helix, 50% strand | — |
| I | Fab S139/1 heavy chain | protein | 186 | 6% helix, 50% strand | — |
| N | Fab S139/1 light chain | protein | 213 | 5% helix, 49% strand | — |
| J | Fab S139/1 heavy chain | protein | 212 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, C, B, E, D, F, H, I, J
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains I, J, H
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains C, E, A
- SO4 · Sulfate ion · ion · 18 copies · chains A, H, B, D, F, C, I, E, J
- GOL · Glycerol · additive · 2 copies · chains A, B, D, C, F
- PG4 · Tetraethylene glycol · additive · chains C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.87 | 0.88 | 130 | empty |
| 2 | 344 | 0.86 | 0.95 | 40 | empty |
| 3 | 924 | 0.74 | 0.78 | 95 | empty |
| 4 | 732 | 0.74 | 0.79 | 56 | SO4 |
| 5 | 741 | 0.73 | 0.79 | 59 | PG4 |
Interfaces
24 interfaces between chains.
- C–D · 2886 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2886 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2871 Ų buried · 38 hydrogen bonds · protein-protein
- N–J · 1909 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1908 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 21 glycan, 3 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4GMS · Crystal structure of heterosubtypic Fab S139/1 in complex with influenza A H3… · the same entry in another collection · chain L against L, 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 P03435
- Elsewhere: RCSB PDB 4GMS · PDBe 4GMS · UniProt P03435
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