MolNFT v1 · #119926 · protein
Crystal structure of H1 hemagglutinin from A/WASHINGTON/05/2011 in complex with a neutralizing antibody 3E1
5GJT: “Crystal structure of H1 hemagglutinin from A/WASHINGTON/05/2011 in complex with a neutralizing antibody 3E1”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.57). MolNFT v1 #119926 on GenesisL1: 3D structure…
- PDB
- 5GJT
- Type
- protein
- Length
- 908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Light chain of human neutralizing antibody 3E1; Heavy chain of human…
- UniProt
- N0C8E5
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 321 | 8% helix, 37% strand | N0C8E5 |
| B | Hemagglutinin | protein | 165 | 54% helix, 16% strand | N0C8E5 |
| L | Light chain of human neutralizing antibody 3E1 | protein | 211 | 5% helix, 48% strand | — |
| H | Heavy chain of human neutralizing antibody 3E1 | protein | 211 | 1% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.57 | 0.81 | 27 | empty |
| 2 | 399 | 0.55 | 0.74 | 56 | empty |
| 3 | 183 | 0.54 | 0.79 | 32 | empty |
| 4 | 186 | 0.47 | 0.75 | 23 | empty |
| 5 | 225 | 0.44 | 0.72 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2852 Ų buried · 41 hydrogen bonds · protein-protein
- L–H · 1827 Ų buried · 17 hydrogen bonds · protein-protein
- B–H · 560 Ų buried · 4 hydrogen bonds · protein-protein
- B–L · 265 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 173 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5GJT · Crystal structure of H1 hemagglutinin from A/Washington/05/2011 in complex with a… · 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 N0C8E5
- Elsewhere: RCSB PDB 5GJT · PDBe 5GJT · UniProt N0C8E5
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