MolNFT v1 · #53554 · protein
Staphylococcus aureus complement subversion protein sbi-IV in complex with complement fragment C3D revealing an alternative binding mode
2WY7 · Complement C3D fragment: “Staphylococcus aureus complement subversion protein sbi-IV in complex with complement fragment C3D revealing…”. X-ray diffraction, 5 pockets (best druggability 0.54). MolNFT v1 #53554 on GenesisL1: 3D…
- PDB
- 2WY7
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3D fragment; IgG-binding protein
- UniProt
- P01024, C8LN82
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3D fragment | protein | 291 | 64% helix, 2% strand | P01024 |
| Q | IgG-binding protein | protein | 66 | 88% helix, 0% strand | C8LN82 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.54 | 0.81 | 22 | GOL |
| 2 | 192 | 0.50 | 0.77 | 28 | GOL |
| 3 | 62 | 0.39 | 0.79 | 12 | empty |
| 4 | 81 | 0.33 | 0.75 | 19 | GOL |
| 5 | 67 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–Q · 686 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2WY7 · Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement… · the same entry in another collection · chain A against A, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A 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 P01024
- Every structure of UniProt C8LN82
- Elsewhere: RCSB PDB 2WY7 · PDBe 2WY7 · UniProt P01024 · UniProt C8LN82
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