MolNFT v1 · #89826 · protein
Crystal structure of C5B-6
4E0S · Complement C5: “Crystal structure of C5B-6”. X-ray diffraction, 6 ligands (NAG, MAN, FUC), 20 pockets (best druggability 0.82). MolNFT v1 #89826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4E0S
- Type
- protein
- Length
- 2,450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Complement component C6
- UniProt
- P01031, P13671
- Ligands
- NAG, MAN, FUC, BGC, NA, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C5 | protein | 1552 | 16% helix, 36% strand | P01031 |
| B | Complement component C6 | protein | 898 | 19% helix, 21% strand | P13671 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
- BGC · beta-D-glucopyranose · sugar · chains B
- NA · Sodium ion · metal · chains A
- CA · Calcium ion · metal · chains B
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 | 1078 | 0.82 | 0.83 | 114 | MAN |
| 2 | 252 | 0.80 | 0.92 | 32 | empty |
| 3 | 272 | 0.77 | 0.89 | 46 | empty |
| 4 | 885 | 0.75 | 0.78 | 92 | empty |
| 5 | 760 | 0.74 | 0.79 | 79 | empty |
Interfaces
1 interface between chains.
- A–B · 3729 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide, 7 glycan (disulfide, C-mannosylation, N-glycosylation, O-glycosylation).
Compared structures
- 4E0S · Crystal Structure of C5b-6 · the same entry in another collection · chain A against A, TM-score 1.00
- P13671 · AlphaFold monomer V2.0 prediction for complement component C6 (P13671) · a predicted model of the same protein · chain B against A, TM-score 0.66
- P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain A against A, TM-score 0.57
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 P01031
- Every structure of UniProt P13671
- Elsewhere: RCSB PDB 4E0S · PDBe 4E0S · UniProt P01031 · UniProt P13671
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