Research workbench
Crystal structure of disulphide-linked human C3D dimer in complex with staphylococcus aureus complement subversion protein sbi-IV
Analyse Crystal structure of disulphide-linked human C3D dimer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RMU
- Type
- protein
- Length
- 727 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Immunoglobulin-binding protein sbi
- UniProt
- P01024, Q931F4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 299 | 65% helix, 2% strand | P01024 |
| C | Immunoglobulin-binding protein sbi | protein | 62 | 84% helix, 0% strand | Q931F4 |
| B | Complement C3 | protein | 300 | 64% helix, 2% strand | P01024 |
| D | Immunoglobulin-binding protein sbi | protein | 66 | 88% helix, 0% strand | Q931F4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.60 | 0.78 | 42 | empty |
| 2 | 222 | 0.58 | 0.80 | 29 | empty |
| 3 | 288 | 0.55 | 0.76 | 27 | empty |
| 4 | 252 | 0.51 | 0.75 | 27 | empty |
| 5 | 155 | 0.46 | 0.76 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2287 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 856 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 804 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6RMU · Crystal structure of disulphide-linked human C3d dimer in complex with Staphylococcus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q931F4 · AlphaFold monomer V2.0 prediction for immunoglobulin-binding protein sbi (Q931F4) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q931F4
- Elsewhere: RCSB PDB 6RMU · PDBe 6RMU · UniProt P01024 · UniProt Q931F4
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