MolNFT v1 · #173770 · protein
C3B in complex with CP40
7BAG · Complement C3: “C3B in complex with CP40”. X-ray diffraction, 5 ligands (EXL, ACM, NAG), 18 pockets (best druggability 0.75). MolNFT v1 #173770 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BAG
- Type
- protein
- Length
- 1,568 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Compstatin CP40
- UniProt
- P01024
- Ligands
- EXL, ACM, NAG, CA, NH2
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 640 | 8% helix, 49% strand | P01024 |
| B | Complement C3 | protein | 915 | 27% helix, 29% strand | P01024 |
| C | Compstatin CP40 | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- EXL · 1-Methyl-L-tryptophan · ligand · chains A, C
- ACM · Acetamide · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- NH2 · Amino group · ion · chains C
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.75 | 0.79 | 58 | empty |
| 2 | 460 | 0.74 | 0.83 | 44 | empty |
| 3 | 830 | 0.71 | 0.76 | 87 | empty |
| 4 | 127 | 0.61 | 0.86 | 24 | empty |
| 5 | 302 | 0.60 | 0.78 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5161 Ų buried · 74 hydrogen bonds · protein-protein
- A–C · 608 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 3 covalent, 2 modified, 1 d-amino, 1 glycan (disulfide, covalent ligand, D-amino acid, N-glycosylation, methylation, nonstandard).
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 P01024
- Elsewhere: RCSB PDB 7BAG · PDBe 7BAG · UniProt P01024
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