Research workbench
C3 convertase (C3BBB) stabilized by scin
Analyse C3 convertase (C3BBB) stabilized by scin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WIN
- Type
- protein
- Length
- 8,518 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3B alpha' chain; Complement factor B…
- EC
- 3.4.21.47
- UniProt
- P01024, P00751, Q6GFB4
- Ligands
- NAG, BMA, MAN, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Complement C3 beta chain | protein | 638 | 7% helix, 49% strand | P01024 |
| B | Complement C3B alpha' chain | protein | 901 | 24% helix, 29% strand | P01024 |
| D | Complement C3B alpha' chain | protein | 901 | 24% helix, 29% strand | P01024 |
| F, H | Complement C3B alpha' chain | protein | 900 | 24% helix, 28% strand | P01024 |
| I, J, K, L | Complement factor B (EC 3.4.21.47) | protein | 507 | 22% helix, 23% strand | P00751 |
| M, N, P, Q | Staphylococcal complement inhibitor | protein | 84 | 83% helix, 0% strand | Q6GFB4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- BMA · beta-D-mannopyranose · sugar · 21 copies · chains E
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains G, A
- MG · Magnesium ion · metal · 4 copies · chains D, I, H, J, F, K, B, L
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 | 901 | 0.81 | 0.83 | 65 | empty |
| 2 | 816 | 0.81 | 0.84 | 70 | empty |
| 3 | 789 | 0.81 | 0.84 | 72 | empty |
| 4 | 986 | 0.81 | 0.82 | 79 | empty |
| 5 | 1037 | 0.80 | 0.81 | 86 | empty |
Interfaces
38 interfaces between chains.
- C–D · 5288 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 5282 Ų buried · 66 hydrogen bonds · protein-protein
- E–F · 5262 Ų buried · 64 hydrogen bonds · protein-protein
- G–H · 5018 Ų buried · 57 hydrogen bonds · protein-protein
- C–E · 1488 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 2WIN · C3 convertase (C3bBb) stabilized by SCIN · the same entry in another collection · chain K against K, TM-score 1.00
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 P00751
- Every structure of UniProt Q6GFB4
- Elsewhere: RCSB PDB 2WIN · PDBe 2WIN · UniProt P01024 · UniProt P00751 · UniProt Q6GFB4
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