Research workbench
L-ficolin complexed to N-acetyl-cystein
Analyse L-ficolin complexed to N-acetyl-cystein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J1G
- Type
- protein
- Length
- 1,279 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficolin-2
- UniProt
- Q15485
- Ligands
- SC2, NAG, BMA, MAN, FUC, CA
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ficolin-2 | protein | 197 | 11% helix, 34% strand | Q15485 |
| B, F | Ficolin-2 | protein | 217 | 15% helix, 33% strand | Q15485 |
| C | Ficolin-2 | protein | 216 | 15% helix, 32% strand | Q15485 |
| D | Ficolin-2 | protein | 214 | 14% helix, 35% strand | Q15485 |
| E | Ficolin-2 | protein | 218 | 15% helix, 33% strand | Q15485 |
Ligands and binding sites
- SC2 · N-acetyl-L-cysteine · ligand · chains E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, E
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
- CA · Calcium ion · metal · 5 copies · chains B, C, D, E, F
- ACT · Acetate ion · additive · 5 copies · chains B, C, E, F
- P4C · O-acetaldehydyl-hexaethylene glycol · additive · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.83 | 0.84 | 115 | P4C, SC2 |
| 2 | 551 | 0.76 | 0.83 | 51 | empty |
| 3 | 244 | 0.70 | 0.86 | 37 | P4C |
| 4 | 277 | 0.65 | 0.82 | 31 | ACT |
| 5 | 337 | 0.62 | 0.79 | 38 | empty |
Interfaces
8 interfaces between chains.
- A–B · 608 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 595 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 550 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 527 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 524 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, additive adduct).
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 2J1G · PDBe 2J1G · UniProt Q15485
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