MolNFT v1 · #4408 · protein
Structure of the Fab fragment from a human IgM cold agglutinin
1DN0 · IgM-kappa cold agglutinin (light chain): “Structure of the Fab fragment from a human IgM cold agglutinin”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #4408 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1DN0
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgM-kappa cold agglutinin (light chain); IgM-kappa cold agglutinin (heavy chain)
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | IgM-kappa cold agglutinin (light chain) | protein | 215 | 7% helix, 50% strand | — |
| B | IgM-kappa cold agglutinin (heavy chain) | protein | 216 | 1% helix, 51% strand | — |
| D | IgM-kappa cold agglutinin (heavy chain) | protein | 217 | 3% helix, 50% strand | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.71 | 0.81 | 43 | empty |
| 2 | 380 | 0.56 | 0.74 | 57 | empty |
| 3 | 350 | 0.56 | 0.75 | 40 | empty |
| 4 | 66 | 0.36 | 0.78 | 15 | empty |
| 5 | 53 | 0.35 | 0.79 | 11 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1787 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1754 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1DN0 · Structure of the Fab fragment from a human 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 1DN0 · PDBe 1DN0
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