MolNFT v1 · #148320 · protein
C1R homodimer CUB1-EGF-CUB2
6F39 · Complement C1R subcomponent: “C1R homodimer CUB1-EGF-CUB2”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.81). MolNFT v1 #148320 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F39
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C1R subcomponent
- EC
- 3.4.21.41
- UniProt
- P00736
- Ligands
- NAG, MAN, BMA, GAL, CA, NA
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C1R subcomponent (EC 3.4.21.41) | protein | 275 | 0% helix, 34% strand | P00736 |
| B | Complement C1R subcomponent (EC 3.4.21.41) | protein | 280 | 1% helix, 30% strand | P00736 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.81 | 0.91 | 40 | empty |
| 2 | 234 | 0.79 | 0.92 | 31 | empty |
| 3 | 1039 | 0.73 | 0.76 | 76 | empty |
| 4 | 997 | 0.73 | 0.76 | 68 | empty |
| 5 | 196 | 0.72 | 0.88 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1019 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 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 P00736
- Elsewhere: RCSB PDB 6F39 · PDBe 6F39 · UniProt P00736
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