Research workbench
Complex of CH28/11 Fab and ssea-4 (tetragonal form)
Analyse Complex of CH28/11 Fab and ssea-4 (tetragonal form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UG7
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CH28/11 Fab light chain; CH28/11 Fab heavy chain
- Ligands
- GAL, BGC, GLA, NGA, SIA, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | CH28/11 Fab light chain | protein | 211 | 6% helix, 51% strand | — |
| H | CH28/11 Fab heavy chain | protein | 213 | 8% helix, 52% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains L, H
- BGC · beta-D-glucopyranose · sugar · chains L
- GLA · alpha-D-galactopyranose · sugar · chains L, H
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains L, H
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains H
- SO4 · Sulfate ion · ion · 4 copies · chains L, H
- EDO · 1,2-ethanediol · additive · 5 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.63 | 0.75 | 74 | empty |
| 2 | 57 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1692 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6UG7 · Complex of ch28/11 Fab and SSEA-4 (tetragonal form) · the same entry in another collection · chain L against L, 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 6UG7 · PDBe 6UG7
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