Research workbench
Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein a from staphylococcus aureus at 2.9-and 2.8-ångströms resolution
Analyse Crystallographic refinement and atomic models of a human Fc fragment and its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FC2
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragment B of protein a complex; Immunoglobulin Fc
- UniProt
- P02976
- Ligands
- NAG, MAN, GAL, FUC, SO4
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Fragment B of protein a complex | protein | 43 | 49% helix, 0% strand | P02976 |
| D | Immunoglobulin Fc | protein | 206 | 9% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains D
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains D
- GAL · beta-D-galactopyranose · sugar · chains D
- FUC · alpha-L-fucopyranose · sugar · chains D
- SO4 · Sulfate ion · ion · chains C, D
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 | 67 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- C–D · 686 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1FC2 · Crystallographic Refinement and Atomic Models of a Human FC Fragment and its Complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- P02976 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P02976) · a predicted model of the same protein · chain C against A, TM-score 0.84
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 P02976
- Elsewhere: RCSB PDB 1FC2 · PDBe 1FC2 · UniProt P02976
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