Research workbench
L-ficolin complexed to sulphates
Analyse L-ficolin complexed to sulphates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R9T
- Type
- protein
- Length
- 649 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficolin-2
- UniProt
- Q15485
- Ligands
- NAG, CA, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ficolin-2 | protein | 218 | 16% helix, 33% strand | Q15485 |
| A | Ficolin-2 | protein | 217 | 14% helix, 33% strand | Q15485 |
| C | Ficolin-2 | protein | 214 | 16% helix, 34% strand | Q15485 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- CA · Calcium ion · metal · 3 copies · chains B, A, C
- SO4 · Sulfate ion · ion · 4 copies · chains B, A, C
- ACT · Acetate ion · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.76 | 0.81 | 83 | empty |
| 2 | 357 | 0.68 | 0.82 | 42 | empty |
| 3 | 322 | 0.59 | 0.77 | 25 | empty |
| 4 | 84 | 0.53 | 0.85 | 21 | empty |
| 5 | 88 | 0.46 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–A · 572 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 502 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 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 Q15485
- Elsewhere: RCSB PDB 4R9T · PDBe 4R9T · UniProt Q15485
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