Research workbench
Crystal structure of a Staphylococcus aureus protein (SSL7) in complex with Fc of human IgA1
Analyse Crystal structure of a Staphylococcus aureus protein (SSL7) in complex with Fc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QEJ
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Homo sapiens; Staphylococcus aureus
- Molecule
- Ig alpha-1 C region; Superantigen-like molecule 7
- UniProt
- P01876, Q2YVR9
- Ligands
- NAG, CA
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · resolution 3.2 · 4 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig alpha-1 C region | protein | 211 | 9% helix, 37% strand | P01876 |
| B | Ig alpha-1 C region | protein | 209 | 12% helix, 36% strand | P01876 |
| C | Superantigen-like molecule 7 | protein | 191 | 20% helix, 35% strand | Q2YVR9 |
| D | Superantigen-like molecule 7 | protein | 192 | 18% helix, 41% strand | Q2YVR9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · chains C
- GOL · Glycerol · additive · 5 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.73 | 0.78 | 74 | empty |
| 2 | 554 | 0.69 | 0.78 | 40 | GOL |
| 3 | 69 | 0.42 | 0.81 | 17 | empty |
| 4 | 94 | 0.40 | 0.77 | 24 | empty |
| 5 | 116 | 0.38 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1358 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 854 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 826 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 106 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2QEJ · Crystal structure of a staphylococcus aureus protein (SSL7) in complex with Fc of human… · the same entry in another collection · chain A against A, TM-score 1.00
- P01876 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant alpha 1 (P01876) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P01876
- Every structure of UniProt Q2YVR9
- Elsewhere: RCSB PDB 2QEJ · PDBe 2QEJ · UniProt P01876 · UniProt Q2YVR9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.