Research workbench
Fc fragment of human IgG in complex with the C domain of staphylococcal protein a mutant - Q9W
Analyse Fc fragment of human IgG in complex with the C domain of staphylococcal protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZNC
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G-binding protein a; Ig gamma-3 chain C region
- UniProt
- P38507, P01860
- Pockets
- 10 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Immunoglobulin G-binding protein a | protein | 53 | 75% helix, 0% strand | P38507 |
| D, E | Ig gamma-3 chain C region | protein | 207 | 11% helix, 48% strand | P01860 |
| F | Ig gamma-3 chain C region | protein | 195 | 12% helix, 47% strand | P01860 |
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.47 | 0.73 | 28 | empty |
| 2 | 72 | 0.45 | 0.82 | 17 | empty |
| 3 | 106 | 0.42 | 0.78 | 23 | empty |
| 4 | 187 | 0.41 | 0.72 | 28 | empty |
| 5 | 87 | 0.41 | 0.78 | 19 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1155 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 758 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 470 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 362 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4ZNC · Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant… · the same entry in another collection · chain F against F, TM-score 1.00
- P01860 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 3 (P01860) · a predicted model of the same protein · chain F against A, TM-score 0.98
- P38507 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P38507) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P38507
- Every structure of UniProt P01860
- Elsewhere: RCSB PDB 4ZNC · PDBe 4ZNC · UniProt P38507 · UniProt P01860
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