Research workbench
L-ficolin complexed to B-1,3-D-glucan
Analyse L-ficolin complexed to B-1,3-D-glucan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J0Y
- Type
- protein
- Length
- 1,261 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficolin-2
- UniProt
- Q15485
- Ligands
- BGC, NAG, BMA, CA
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ficolin-2 | protein | 193 | 13% helix, 31% strand | Q15485 |
| B, E | Ficolin-2 | protein | 218 | 16% helix, 32% strand | Q15485 |
| C, F | Ficolin-2 | protein | 215 | 14% helix, 33% strand | Q15485 |
| D | Ficolin-2 | protein | 202 | 13% helix, 31% strand | Q15485 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 9 copies · chains C, F, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, E, C, F
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 6 copies · chains B, C, E, F
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.82 | 0.83 | 113 | empty |
| 2 | 559 | 0.76 | 0.83 | 52 | empty |
| 3 | 293 | 0.68 | 0.83 | 36 | empty |
| 4 | 211 | 0.62 | 0.83 | 30 | empty |
| 5 | 82 | 0.51 | 0.84 | 18 | empty |
Interfaces
8 interfaces between chains.
- D–E · 575 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 535 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 492 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 4 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 2J0Y · PDBe 2J0Y · UniProt Q15485
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