Research workbench
Hef-mut with TR323 complex
Analyse Hef-mut with TR323 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E62
- Type
- protein
- Length
- 1,146 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase
- UniProt
- K9LG83
- Ligands
- Z3Q, 5N6, NAG, MAN, BMA, GAL
- Pockets
- 9 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin-esterase | protein | 424 | 14% helix, 35% strand | K9LG83 |
| B, D | Hemagglutinin-esterase | protein | 149 | 47% helix, 13% strand | K9LG83 |
Ligands and binding sites
- Z3Q · 2-azidoethyl 2-acetamido-2-deoxy-beta-D-glucopyranoside · ligand · 2 copies
- 5N6 · 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, D, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, C
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.55 | 0.77 | 31 | empty |
| 2 | 266 | 0.51 | 0.74 | 36 | empty |
| 3 | 210 | 0.49 | 0.75 | 38 | empty |
| 4 | 120 | 0.45 | 0.78 | 22 | empty |
| 5 | 90 | 0.39 | 0.77 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3340 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3280 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 641 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5E62 · HEF-mut with Tr323 complex · 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 K9LG83
- Elsewhere: RCSB PDB 5E62 · PDBe 5E62 · UniProt K9LG83
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