Research workbench
Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/VIET NAM/1203/2004 (H5N1)
Analyse Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MHH
- Type
- protein
- Length
- 2,820 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; H5M9 antibody, light chain (kappa); Hemagglutinin HA2 chain…
- UniProt
- Q6DQ33
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 324 | 10% helix, 38% strand | Q6DQ33 |
| L, I, K | H5M9 antibody, light chain (kappa) | protein | 217 | 5% helix, 47% strand | — |
| B, D, F | Hemagglutinin HA2 chain | protein | 177 | 57% helix, 13% strand | Q6DQ33 |
| H, G, J | H5M9 antibody, heavy chain (IGG1) | protein | 222 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, C, B, E, D, F, L, I, K
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.86 | 0.90 | 92 | empty |
| 2 | 88 | 0.77 | 0.98 | 15 | empty |
| 3 | 382 | 0.76 | 0.86 | 35 | empty |
| 4 | 271 | 0.70 | 0.85 | 29 | empty |
| 5 | 391 | 0.63 | 0.78 | 55 | empty |
Interfaces
24 interfaces between chains.
- E–F · 2531 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2485 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2476 Ų buried · 38 hydrogen bonds · protein-protein
- K–J · 2096 Ų buried · 23 hydrogen bonds · protein-protein
- L–H · 2064 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 4MHH · Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/Viet… · 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 Q6DQ33
- Elsewhere: RCSB PDB 4MHH · PDBe 4MHH · UniProt Q6DQ33
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