Research workbench
Genomic and structural basis for the human anti-alpha-galactosyl antibody response
Analyse Genomic and structural basis for the human anti-alpha-galactosyl antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UEM
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain Fab of antibody HKB7; Heavy chain Fab arm of antibody HKB7
- Ligands
- GAL, GLA, CL
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, L | Light chain Fab of antibody HKB7 | protein | 216 | 6% helix, 52% strand | — |
| D | Heavy chain Fab arm of antibody HKB7 | protein | 218 | 11% helix, 51% strand | — |
| H | Heavy chain Fab arm of antibody HKB7 | protein | 219 | 8% helix, 52% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains H, L, C, D
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains H, L, C, D
- CL · Chloride ion · ion · 15 copies · chains C, D, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.67 | 0.77 | 57 | empty |
| 2 | 638 | 0.64 | 0.74 | 68 | CL |
| 3 | 649 | 0.63 | 0.74 | 68 | CL |
| 4 | 64 | 0.59 | 0.90 | 19 | empty |
| 5 | 80 | 0.31 | 0.74 | 20 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1890 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1851 Ų buried · 17 hydrogen bonds · protein-protein
- C–L · 489 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 153 Ų buried · 0 hydrogen bonds · protein-protein
- D–L · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7UEM · Genomic and structural basis for the human anti-alpha-galactosyl antibody response · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 7UEM · PDBe 7UEM
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