Research workbench
CD22 D6-D7 in complex with Fab M971
Analyse CD22 D6-D7 in complex with Fab M971 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O52
- Type
- protein
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M971 Fab heavy chain; M971 Fab light chain; CD22 D6-D7 ig domains
- Ligands
- NAG, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | M971 Fab heavy chain | protein | 227 | 7% helix, 54% strand | — |
| L | M971 Fab light chain | protein | 215 | 7% helix, 52% strand | — |
| U | CD22 D6-D7 ig domains | protein | 162 | 4% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains U
- SO4 · Sulfate ion · ion · 5 copies · chains H, U, L
- GOL · Glycerol · additive · 3 copies · chains L, U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.67 | 0.75 | 67 | empty |
| 2 | 148 | 0.47 | 0.77 | 32 | empty |
| 3 | 51 | 0.40 | 0.82 | 23 | empty |
| 4 | 100 | 0.37 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1988 Ų buried · 16 hydrogen bonds · protein-protein
- H–U · 797 Ų buried · 15 hydrogen bonds · protein-protein
- L–U · 286 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7O52 · CD22 d6-d7 in complex with Fab m971 · the same entry in another collection · chain H against H, 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 7O52 · PDBe 7O52
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