Research workbench
H-ficolin complexed to D-fucose
Analyse H-ficolin complexed to D-fucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J60
- Type
- protein
- Length
- 638 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficolin-3
- UniProt
- O75636
- Ligands
- ABE, CA
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ficolin-3 | protein | 214 | 15% helix, 28% strand | O75636 |
| B | Ficolin-3 | protein | 213 | 16% helix, 31% strand | O75636 |
| C | Ficolin-3 | protein | 211 | 16% helix, 27% strand | O75636 |
Ligands and binding sites
- ABE · alpha-D-Abequopyranose · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.73 | 0.77 | 80 | empty |
| 2 | 233 | 0.54 | 0.78 | 26 | empty |
| 3 | 141 | 0.41 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 513 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
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 O75636
- Elsewhere: RCSB PDB 2J60 · PDBe 2J60 · UniProt O75636
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