MolNFT v1 · #121782 · protein
Structure of complement C5 in complex with eculizumab
5I5K: “Structure of complement C5 in complex with eculizumab”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #121782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I5K
- Type
- protein
- Length
- 4,134 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Eculizumab heavy chain (variable domain); Eculizumab light chain (variable…
- UniProt
- P01031
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Complement C5 | protein | 1634 | 19% helix, 36% strand | P01031 |
| H, X | Eculizumab heavy chain (variable domain) | protein | 221 | 4% helix, 49% strand | — |
| L, Y | Eculizumab light chain (variable domain) | protein | 213 | 1% helix, 48% strand | — |
| A | Complement C5 | protein | 1632 | 19% helix, 35% strand | P01031 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 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 | 971 | 0.84 | 0.85 | 100 | empty |
| 2 | 855 | 0.83 | 0.85 | 89 | empty |
| 3 | 842 | 0.80 | 0.82 | 77 | empty |
| 4 | 693 | 0.78 | 0.82 | 61 | empty |
| 5 | 570 | 0.73 | 0.81 | 55 | empty |
Interfaces
7 interfaces between chains.
- X–Y · 1889 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1852 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 1432 Ų buried · 14 hydrogen bonds · protein-protein
- A–X · 700 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 696 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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
- Elsewhere: RCSB PDB 5I5K · PDBe 5I5K · UniProt P01031
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