Research workbench
Crystal structure of Fab CR6261 in complex with a H5N1 influenza virus hemagglutinin.
Analyse Crystal structure of Fab CR6261 in complex with a H5N1 influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GBM
- Type
- protein
- Length
- 1,829 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody (Fab)
- UniProt
- Q6DQ33
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.59
Structure
x-ray diffraction · 8 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 324 | 10% helix, 40% strand | Q6DQ33 |
| B | Hemagglutinin | protein | 177 | 58% helix, 13% strand | Q6DQ33 |
| C | Hemagglutinin | protein | 323 | 10% helix, 39% strand | Q6DQ33 |
| D | Hemagglutinin | protein | 173 | 55% helix, 13% strand | Q6DQ33 |
| H | Antibody (Fab) | protein | 214 | 4% helix, 50% strand | — |
| L | Antibody (Fab) | protein | 208 | 9% helix, 47% strand | — |
| I | Antibody (Fab) | protein | 213 | 7% helix, 50% strand | — |
| M | Antibody (Fab) | protein | 197 | 7% helix, 39% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, B, L, D, M
- BMA · beta-D-mannopyranose · sugar · 2 copies
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.59 | 0.78 | 41 | empty |
| 2 | 300 | 0.56 | 0.76 | 33 | GOL |
| 3 | 291 | 0.56 | 0.76 | 42 | empty |
| 4 | 287 | 0.55 | 0.76 | 31 | empty |
| 5 | 75 | 0.50 | 0.84 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2464 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2426 Ų buried · 41 hydrogen bonds · protein-protein
- H–L · 1615 Ų buried · 12 hydrogen bonds · protein-protein
- I–M · 1607 Ų buried · 11 hydrogen bonds · protein-protein
- D–I · 578 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 3GBM · Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin. · 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 Q6DQ33
- Elsewhere: RCSB PDB 3GBM · PDBe 3GBM · UniProt Q6DQ33
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