MolNFT v1 · #137279 · protein
Crystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S) from the influenza virus A/SHANGHAI/2/2013 (H7N9) with lsta
5VJM · Hemagglutinin HA1: “Crystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S) from the influenza virus A/SHANGHAI/2/2013…”. X-ray diffraction, 2 ligands (NAG, SIA), 3 pockets (best druggability 0.60). MolNFT v1 #137279 on…
- PDB
- 5VJM
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- R4NN21
- Ligands
- NAG, SIA
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 314 | 9% helix, 41% strand | R4NN21 |
| B | Hemagglutinin HA2 | protein | 171 | 55% helix, 13% strand | R4NN21 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- MOH · Methanol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.60 | 0.80 | 25 | empty |
| 2 | 78 | 0.43 | 0.81 | 19 | empty |
| 3 | 95 | 0.42 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2963 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5VJM · Crystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S) from the influenza… · 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 R4NN21
- Elsewhere: RCSB PDB 5VJM · PDBe 5VJM · UniProt R4NN21
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