MolNFT v1 · #69299 · protein
Structure of complement C5 in complex with the C-terminal beta-grasp domain of SSL7
3KM9: “Structure of complement C5 in complex with the C-terminal beta-grasp domain of SSL7”. X-ray diffraction, 2 ligands (NAG, CD), 20 pockets (best druggability 0.84). MolNFT v1 #69299 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3KM9
- Type
- protein
- Length
- 3,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Staphylococcal enterotoxin-like toxin
- UniProt
- P01031, A6QE84
- Ligands
- NAG, CD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Complement C5 | protein | 1459 | 18% helix, 28% strand | P01031 |
| X, Y | Staphylococcal enterotoxin-like toxin | protein | 102 | 18% helix, 35% strand | A6QE84 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CD · Cadmium ion · metal · 5 copies · chains A, 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 | 785 | 0.84 | 0.87 | 87 | empty |
| 2 | 951 | 0.83 | 0.85 | 85 | CD |
| 3 | 1007 | 0.79 | 0.80 | 107 | empty |
| 4 | 1111 | 0.79 | 0.80 | 110 | empty |
| 5 | 578 | 0.78 | 0.84 | 87 | empty |
Interfaces
3 interfaces between chains.
- B–Y · 1061 Ų buried · 12 hydrogen bonds · protein-protein
- A–X · 1060 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 305 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3KM9 · Structure of complement C5 in complex with the C-terminal beta-grasp domain of SSL7 · the same entry in another collection · chain A against A, TM-score 1.00
- P01031 · AlphaFold monomer V2.0 prediction for complement C5 (P01031) · a predicted model of the same protein · chain A 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 P01031
- Every structure of UniProt A6QE84
- Elsewhere: RCSB PDB 3KM9 · PDBe 3KM9 · UniProt P01031 · UniProt A6QE84
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