MolNFT v1 · #53031 · protein
Complement C3B in complex with factor H domains 1-4
2WII · Complement C3 beta chain: “Complement C3B in complex with factor H domains 1-4”. X-ray diffraction, 3 ligands (BMA, NAG, CA), 20 pockets (best druggability 0.82). MolNFT v1 #53031 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2WII
- Type
- protein
- Length
- 1,781 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3 beta chain; Complement C3B alpha' chain; Complement factor H
- UniProt
- P01024, P08603
- Ligands
- BMA, NAG, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 beta chain | protein | 640 | 8% helix, 52% strand | P01024 |
| B | Complement C3B alpha' chain | protein | 896 | 28% helix, 32% strand | P01024 |
| C | Complement factor H | protein | 245 | 0% helix, 40% strand | P08603 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 4 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 17 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.82 | 0.83 | 95 | GOL |
| 2 | 939 | 0.76 | 0.79 | 76 | empty |
| 3 | 1062 | 0.75 | 0.78 | 115 | empty |
| 4 | 753 | 0.71 | 0.77 | 58 | GOL |
| 5 | 514 | 0.69 | 0.79 | 58 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 5325 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 1527 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1013 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2WII · Complement C3b in complex with factor H domains 1-4 · 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 0.99
- P08603 · AlphaFold monomer V2.0 prediction for complement factor H (P08603) · a predicted model of the same protein · chain C against A, TM-score 0.73
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 P08603
- Elsewhere: RCSB PDB 2WII · PDBe 2WII · UniProt P01024 · UniProt P08603
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