Research workbench
X-ray crystal structure of covalent-bonded complex of Fc and peptide
Analyse X-ray crystal structure of covalent-bonded complex of Fc and peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IQH
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain; 17-mer peptide (gpdcayhkgelvwctfh)
- UniProt
- P0DOX5
- Ligands
- GUA, NAG, MAN, BMA, FUC
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin gamma-1 heavy chain | protein | 207 | 10% helix, 44% strand | P0DOX5 |
| C, D | 17-mer peptide (gpdcayhkgelvwctfh) | protein | 13 | 0% helix, 69% strand | — |
Ligands and binding sites
- GUA · Glutaric acid · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–B · 1181 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 621 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 588 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6IQH · X-ray crystal structure of covalent-bonded complex of Fc and peptide · 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 P0DOX5
- Elsewhere: RCSB PDB 6IQH · PDBe 6IQH · UniProt P0DOX5
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