Research workbench
Staphylococcal complement inhibitor (scin) in complex with human complement component C3C
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
- 3L3O
- Type
- protein
- Length
- 2,402 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Staphylococcal complement inhibitor
- UniProt
- P01024, Q931M7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Complement C3 | protein | 639 | 6% helix, 49% strand | P01024 |
| B, E | Complement C3 | protein | 184 | 2% helix, 53% strand | P01024 |
| M, P | Staphylococcal complement inhibitor | protein | 84 | 81% helix, 0% strand | Q931M7 |
| F, C | Complement C3 | protein | 294 | 16% helix, 38% strand | P01024 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.82 | 0.83 | 83 | empty |
| 2 | 94 | 0.74 | 0.96 | 25 | empty |
| 3 | 89 | 0.73 | 0.95 | 20 | empty |
| 4 | 793 | 0.73 | 0.78 | 66 | empty |
| 5 | 424 | 0.72 | 0.83 | 42 | empty |
Interfaces
18 interfaces between chains.
- D–E · 3554 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3552 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 1379 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1170 Ų buried · 12 hydrogen bonds · protein-protein
- F–E · 1166 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3L3O · Staphylococcal Complement Inhibitor (SCIN) in complex with Human Complement Component C3c · the same entry in another collection · chain E against E, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain D 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 3L3O · PDBe 3L3O · UniProt P01024 · UniProt Q931M7
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