MolNFT v1 · #122665 · protein
Anti-CD20 monoclonal antibody Fc fragment
5IW6 · Ig gamma-1 chain C region: “Anti-CD20 monoclonal antibody Fc fragment”. X-ray diffraction, 4 ligands (NAG, BMA, GAL), 2 pockets (best druggability 0.38). MolNFT v1 #122665 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IW6
- Type
- protein
- Length
- 407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region
- UniProt
- P01857
- Ligands
- NAG, BMA, GAL, MAN
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 209 | 11% helix, 48% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 198 | 12% helix, 42% strand | P01857 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.38 | 0.79 | 18 | empty |
| 2 | 67 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1148 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5IW6 · anti-CD20 monoclonal antibody Fc fragment · 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
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 5IW6 · PDBe 5IW6 · UniProt P01857
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