MolNFT v1 · #74007 · protein
Crystal structure of human complement component C8
3OJY · Complement component C8 alpha chain: “Crystal structure of human complement component C8”. X-ray diffraction, 2 ligands (BMA, CA), 17 pockets (best druggability 0.88). MolNFT v1 #74007 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3OJY
- Type
- protein
- Length
- 1,147 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement component C8 alpha chain; Complement component C8 beta chain; Complement…
- UniProt
- P07357, P07358, P07360
- Ligands
- BMA, CA
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement component C8 alpha chain | protein | 478 | 21% helix, 26% strand | P07357 |
| B | Complement component C8 beta chain | protein | 504 | 19% helix, 26% strand | P07358 |
| C | Complement component C8 gamma chain | protein | 165 | 13% helix, 44% strand | P07360 |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.88 | 0.93 | 107 | empty |
| 2 | 357 | 0.83 | 0.92 | 70 | empty |
| 3 | 997 | 0.73 | 0.76 | 77 | BMA |
| 4 | 290 | 0.69 | 0.84 | 35 | empty |
| 5 | 304 | 0.62 | 0.79 | 34 | BMA |
Interfaces
2 interfaces between chains.
- A–B · 2995 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 1242 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 8 glycan, 1 modified (disulfide, C-mannosylation, phosphorylation).
Compared structures
- 3OJY · Crystal Structure of Human Complement Component C8 · the same entry in another collection · chain A against A, TM-score 1.00
- P07357 · AlphaFold monomer V2.0 prediction for complement component C8 alpha chain (P07357) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P07358 · AlphaFold monomer V2.0 prediction for complement component C8 beta chain (P07358) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P07360 · AlphaFold monomer V2.0 prediction for complement component C8 gamma chain (P07360) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P07357
- Every structure of UniProt P07358
- Every structure of UniProt P07360
- Elsewhere: RCSB PDB 3OJY · PDBe 3OJY · UniProt P07357 · UniProt P07358 · UniProt P07360
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