MolNFT v1 · #92114 · protein
Complement C4 in complex with masp-2
4FXG · Complement C4 beta chain: “Complement C4 in complex with masp-2”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #92114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4FXG
- Type
- protein
- Length
- 4,130 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C4 beta chain; Complement C4-a alpha chain; Complement C4 gamma chain…
- EC
- 3.4.21.104
- UniProt
- P0C0L4, O00187
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Complement C4 beta chain | protein | 651 | 5% helix, 43% strand | P0C0L4 |
| B, E | Complement C4-a alpha chain | protein | 740 | 34% helix, 20% strand | P0C0L4 |
| C, F | Complement C4 gamma chain | protein | 287 | 15% helix, 36% strand | P0C0L4 |
| G, I | Mannan-binding lectin serine protease 2 a chain (EC 3.4.21.104) | protein | 145 | 0% helix, 37% strand | O00187 |
| H, J | Mannan-binding lectin serine protease 2 B chain (EC 3.4.21.104) | protein | 242 | 12% helix, 35% strand | O00187 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, D, E
- BMA · beta-D-mannopyranose · sugar · 6 copies
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 | 993 | 0.85 | 0.86 | 113 | empty |
| 2 | 771 | 0.84 | 0.87 | 104 | empty |
| 3 | 445 | 0.78 | 0.86 | 46 | empty |
| 4 | 225 | 0.77 | 0.91 | 29 | empty |
| 5 | 211 | 0.77 | 0.91 | 28 | empty |
Interfaces
18 interfaces between chains.
- D–E · 4694 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 4641 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 4471 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 4417 Ų buried · 50 hydrogen bonds · protein-protein
- B–J · 1145 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 6 glycan, 4 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- O00187 · AlphaFold monomer V2.0 prediction for mannan-binding lectin serine protease 2 (O00187) · a predicted model of the same protein · chain H against A, TM-score 0.97
- P0C0L4 · AlphaFold monomer V2.0 prediction for complement C4-a (P0C0L4) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0C0L4
- Every structure of UniProt O00187
- Elsewhere: RCSB PDB 4FXG · PDBe 4FXG · UniProt P0C0L4 · UniProt O00187
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