MolNFT v1 · #119178 · protein
Crystal structure of human complement C3B in complex with mcp (CCP1-4)
5FO8: “Crystal structure of human complement C3B in complex with mcp (CCP1-4)”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.77). MolNFT v1 #119178 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FO8
- Type
- protein
- Length
- 1,662 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Membrane cofactor protein
- EC
- 3.4.21.47
- UniProt
- P01024, P15529
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 (EC 3.4.21.47) | protein | 639 | 8% helix, 50% strand | P01024 |
| B | Complement C3 (EC 3.4.21.47) | protein | 894 | 29% helix, 32% strand | P01024 |
| C | Membrane cofactor protein | protein | 129 | 2% helix, 39% strand | P15529 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.77 | 0.79 | 103 | EDO |
| 2 | 506 | 0.74 | 0.82 | 43 | empty |
| 3 | 1015 | 0.74 | 0.77 | 75 | EDO |
| 4 | 70 | 0.69 | 0.96 | 23 | empty |
| 5 | 195 | 0.68 | 0.86 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5050 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 694 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 631 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5FO8 · Crystal Structure of Human Complement C3b in Complex with MCP (CCP1-4) · the same entry in another collection · chain A against A, TM-score 1.00
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P15529 · AlphaFold monomer V2.0 prediction for membrane cofactor protein (P15529) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P01024
- Every structure of UniProt P15529
- Elsewhere: RCSB PDB 5FO8 · PDBe 5FO8 · UniProt P01024 · UniProt P15529
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