Research workbench
Crystal structure of complement C3B in complex with factor B
Analyse Crystal structure of complement C3B in complex with factor B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XWJ
- Type
- protein
- Length
- 9,013 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3 alpha chain; Complement factor B
- UniProt
- P01024, P00751
- Ligands
- NAG, NI
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Complement C3 beta chain | protein | 640 | 6% helix, 46% strand | P01024 |
| B, D, F, H | Complement C3 alpha chain | protein | 901 | 24% helix, 28% strand | P01024 |
| I | Complement factor B | protein | 712 | 20% helix, 27% strand | P00751 |
| J, K | Complement factor B | protein | 713 | 20% helix, 25% strand | P00751 |
| L | Complement factor B | protein | 711 | 20% helix, 27% strand | P00751 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, C, D, E, F, G, H, I, J, K, L
- NI · Nickel (II) ion · metal · 4 copies · chains B, I, D, J, F, K, H, 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 | 1062 | 0.89 | 0.90 | 125 | empty |
| 2 | 1000 | 0.88 | 0.90 | 120 | empty |
| 3 | 899 | 0.87 | 0.89 | 104 | empty |
| 4 | 871 | 0.87 | 0.90 | 97 | empty |
| 5 | 858 | 0.85 | 0.88 | 73 | empty |
Interfaces
23 interfaces between chains.
- G–H · 5164 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 5091 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 5083 Ų buried · 62 hydrogen bonds · protein-protein
- E–F · 5059 Ų buried · 59 hydrogen bonds · protein-protein
- B–I · 2746 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2XWJ · Crystal Structure of Complement C3b in Complex with Factor B · the same entry in another collection · chain L against L, 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
- Elsewhere: RCSB PDB 2XWJ · PDBe 2XWJ · UniProt P01024 · UniProt P00751
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