MolNFT v1 · #109229 · protein
Crystal structure of the C domain of staphylococcal protein a in complex with the Fc fragment of human IgG at 2.3 ångström resolution
4WWI · Immunoglobulin G-binding protein a: “Crystal structure of the C domain of staphylococcal protein a in complex with the Fc fragment of human IgG at…”. X-ray diffraction, 7 pockets (best druggability 0.55). MolNFT v1 #109229 on…
- PDB
- 4WWI
- Type
- protein
- Length
- 755 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
- 7 · best druggability 0.55
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin G-binding protein a | protein | 57 | 74% helix, 0% strand | P38507 |
| B | Immunoglobulin G-binding protein a | protein | 56 | 75% helix, 0% strand | P38507 |
| C | Immunoglobulin G-binding protein a | protein | 55 | 75% helix, 0% strand | P38507 |
| D | Ig gamma-3 chain C region | protein | 201 | 11% helix, 46% strand | P01860 |
| E | Ig gamma-3 chain C region | protein | 179 | 12% helix, 44% strand | P01860 |
| F | Ig gamma-3 chain C region | protein | 207 | 10% helix, 49% strand | P01860 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.55 | 0.79 | 30 | empty |
| 2 | 161 | 0.46 | 0.76 | 30 | empty |
| 3 | 164 | 0.41 | 0.73 | 23 | empty |
| 4 | 57 | 0.37 | 0.79 | 15 | empty |
| 5 | 131 | 0.37 | 0.73 | 20 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1144 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 872 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 723 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 378 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 344 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4WWI · Crystal structure of the C domain of staphylococcal protein A in complex with the Fc… · 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 E 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 C against A, TM-score 0.92
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 4WWI · PDBe 4WWI · UniProt P38507 · UniProt P01860
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