MolNFT v1 · #13290 · protein
Fc fragment of rituximab bound to a minimized version of the B-domain from protein a called Z34C
1L6X · Immunoglobulin gamma-1 heavy chain constant region: “Fc fragment of rituximab bound to a minimized version of the B-domain from protein a called Z34C”. X-ray diffraction, 5 ligands (NAG, MAN, GAL), 1 pocket (best druggability 0.33).…
- PDB
- 1L6X
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain constant region; Minimized B-domain of protein a Z34C
- Ligands
- NAG, MAN, GAL, BMA, FUL
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain constant region | protein | 207 | 11% helix, 48% strand | — |
| B | Minimized B-domain of protein a Z34C | protein | 34 | 74% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- FUL · beta-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.33 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 739 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1L6X · Fc fragment of rituximab bound to a minimized version of the B-domain from protein a… · 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 1L6X · PDBe 1L6X
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