Research workbench
Crystal structure of complement C3B in complex with factors B and D
Analyse Crystal structure of complement C3B in complex with factors B and D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XWB
- Type
- protein
- Length
- 4,963 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3B beta chain; Complement C3B alpha' chain; Complement factor B; Complement…
- EC
- 3.4.21.47, 3.4.21.46
- UniProt
- P01024, P00751, P00746
- Ligands
- NAG, BMA, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Complement C3B beta chain | protein | 640 | 6% helix, 48% strand | P01024 |
| B, D | Complement C3B alpha' chain | protein | 901 | 24% helix, 29% strand | P01024 |
| F | Complement factor B (EC 3.4.21.47) | protein | 714 | 19% helix, 28% strand | P00751 |
| H | Complement factor B (EC 3.4.21.47) | protein | 711 | 19% helix, 29% strand | P00751 |
| I, J | Complement factor D (EC 3.4.21.46) | protein | 228 | 8% helix, 33% strand | P00746 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B, C, F, H, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, F, D, H
- GOL · Glycerol · additive · 2 copies · chains I, J
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 | 560 | 0.85 | 0.91 | 64 | empty |
| 2 | 565 | 0.84 | 0.90 | 66 | empty |
| 3 | 522 | 0.84 | 0.90 | 65 | empty |
| 4 | 1105 | 0.83 | 0.85 | 98 | empty |
| 5 | 459 | 0.82 | 0.90 | 55 | empty |
Interfaces
10 interfaces between chains.
- C–D · 5261 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 5187 Ų buried · 59 hydrogen bonds · protein-protein
- B–F · 2604 Ų buried · 45 hydrogen bonds · protein-protein
- D–H · 2598 Ų buried · 43 hydrogen bonds · protein-protein
- F–I · 1105 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 2XWB · Crystal Structure of Complement C3b in complex with Factors B and D · the same entry in another collection · chain J against J, TM-score 1.00
- P00746 · AlphaFold monomer V2.0 prediction for complement factor D (P00746) · a predicted model of the same protein · chain J against A, TM-score 0.99
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P00746
- Elsewhere: RCSB PDB 2XWB · PDBe 2XWB · UniProt P01024 · UniProt P00751 · UniProt P00746
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.