Research workbench
Staphylococcal complement inhibitor (scin) in complex with human complement component C3B
Analyse Staphylococcal complement inhibitor (scin) in complex with human complement… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L5N
- Type
- protein
- Length
- 1,609 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Staphylococcal complement inhibitor
- UniProt
- P01024, Q931M7
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 634 | 3% helix, 37% strand | P01024 |
| B | Complement C3 | protein | 891 | 14% helix, 24% strand | P01024 |
| M | Staphylococcal complement inhibitor | protein | 84 | 0% helix, 0% strand | Q931M7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.78 | 0.97 | 25 | empty |
| 2 | 100 | 0.77 | 0.97 | 28 | empty |
| 3 | 1020 | 0.74 | 0.77 | 68 | empty |
| 4 | 384 | 0.72 | 0.83 | 48 | empty |
| 5 | 76 | 0.72 | 0.96 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5411 Ų buried · 65 hydrogen bonds · protein-protein
- B–M · 761 Ų buried · 6 hydrogen bonds · protein-protein
- A–M · 237 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3L5N · Staphylococcal Complement Inhibitor (SCIN) in complex with Human Complement Component C3b · 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 0.97
- Q931M7 · AlphaFold monomer V2.0 prediction for staphylococcal complement inhibitor (Q931M7) · a predicted model of the same protein · chain M against A, TM-score 0.94
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 P01024
- Every structure of UniProt Q931M7
- Elsewhere: RCSB PDB 3L5N · PDBe 3L5N · UniProt P01024 · UniProt Q931M7
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