Research workbench
Staphylococcal complement inhibitor (scin) in complex with human complement C3C
Analyse Staphylococcal complement inhibitor (scin) in complex with human complement C3C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NMS
- Type
- protein
- Length
- 1,203 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Staphylococcal complement inhibitor
- UniProt
- P01024, Q931M7
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 641 | 6% helix, 49% strand | P01024 |
| C | Complement C3 | protein | 294 | 16% helix, 35% strand | P01024 |
| M | Staphylococcal complement inhibitor | protein | 84 | 76% helix, 0% strand | Q931M7 |
| B | Complement C3 | protein | 184 | 0% helix, 48% strand | P01024 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.81 | 0.82 | 101 | empty |
| 2 | 417 | 0.67 | 0.80 | 40 | empty |
| 3 | 439 | 0.67 | 0.79 | 53 | empty |
| 4 | 51 | 0.67 | 0.97 | 21 | empty |
| 5 | 86 | 0.63 | 0.89 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3596 Ų buried · 58 hydrogen bonds · protein-protein
- C–B · 1186 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 749 Ų buried · 7 hydrogen bonds · protein-protein
- M–B · 704 Ų buried · 9 hydrogen bonds · protein-protein
- A–M · 182 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3NMS · Staphylococcal Complement Inhibitor (SCIN) in complex with Human Complement C3c · the same entry in another collection · chain B against B, 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 0.98
- Q931M7 · AlphaFold monomer V2.0 prediction for staphylococcal complement inhibitor (Q931M7) · a predicted model of the same protein · chain M against A, TM-score 0.97
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 Q931M7
- Elsewhere: RCSB PDB 3NMS · PDBe 3NMS · UniProt P01024 · UniProt Q931M7
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