MolNFT v1 · #19486 · protein
Crystal structure of the Fab fragment of a human monoclonal IgM cold agglutinin
1QLR · IgM kappa chain V-III (kau cold agglutinin): “Crystal structure of the Fab fragment of a human monoclonal IgM cold agglutinin”. X-ray diffraction, 2 ligands (NAG, FUC), 7 pockets (best druggability 0.74). MolNFT v1 #19486 on…
- PDB
- 1QLR
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgM kappa chain V-III (kau cold agglutinin); IgM Fab region IV-J(H4)-C (kau cold…
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | IgM kappa chain V-III (kau cold agglutinin) | protein | 215 | 8% helix, 49% strand | — |
| B, D | IgM Fab region IV-J(H4)-C (kau cold agglutinin) | protein | 209 | 3% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.74 | 0.82 | 44 | empty |
| 2 | 354 | 0.55 | 0.74 | 46 | empty |
| 3 | 269 | 0.52 | 0.75 | 36 | empty |
| 4 | 66 | 0.32 | 0.75 | 18 | empty |
| 5 | 66 | 0.32 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1736 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1707 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 290 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1QLR · CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A HUMAN MONOCLONAL IgM COLD AGGLUTININ · 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
- Elsewhere: RCSB PDB 1QLR · PDBe 1QLR
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