MolNFT v1 · #148254 · protein
C1RC1S complex
6F1C · Complement C1R subcomponent: “C1RC1S complex”. X-ray diffraction, 6 ligands (NAG, BMA, MAN), 14 pockets (best druggability 0.71). MolNFT v1 #148254 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F1C
- Type
- protein
- Length
- 1,130 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C1R subcomponent; Complement C1S subcomponent
- EC
- 3.4.21.41, 3.4.21.42
- UniProt
- P00736, P09871
- Ligands
- NAG, BMA, MAN, GAL, CA, NA
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C1R subcomponent (EC 3.4.21.41) | protein | 291 | 1% helix, 41% strand | P00736 |
| C | Complement C1R subcomponent (EC 3.4.21.41) | protein | 287 | 2% helix, 42% strand | P00736 |
| D | Complement C1S subcomponent (EC 3.4.21.42) | protein | 276 | 1% helix, 48% strand | P09871 |
| B | Complement C1S subcomponent (EC 3.4.21.42) | protein | 276 | 1% helix, 49% strand | P09871 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, D, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- GAL · beta-D-galactopyranose · sugar
- CA · Calcium ion · metal · 12 copies · chains A, C, D, B
- NA · Sodium ion · metal · 6 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.71 | 0.80 | 44 | empty |
| 2 | 454 | 0.66 | 0.78 | 45 | empty |
| 3 | 232 | 0.60 | 0.80 | 37 | empty |
| 4 | 368 | 0.60 | 0.77 | 32 | empty |
| 5 | 307 | 0.54 | 0.75 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1428 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1357 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6F1C · C1rC1s complex · the same entry in another collection · chain B against B, TM-score 1.00
- P00736 · AlphaFold monomer V2.0 prediction for complement C1R subcomponent (P00736) · a predicted model of the same protein · chain C against A, TM-score 0.70
- P09871 · AlphaFold monomer V2.0 prediction for complement C1S subcomponent (P09871) · a predicted model of the same protein · chain B against A, TM-score 0.64
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
- Every structure of UniProt P09871
- Elsewhere: RCSB PDB 6F1C · PDBe 6F1C · UniProt P00736 · UniProt P09871
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