Research workbench
Structure of globular heads of M-ficolin at acidic pH
Analyse Structure of globular heads of M-ficolin at acidic pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JHH
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficolin-1
- UniProt
- O00602
- Ligands
- CA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ficolin-1 | protein | 208 | 16% helix, 30% strand | O00602 |
| F | Ficolin-1 | protein | 209 | 15% helix, 32% strand | O00602 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.62 | 0.79 | 34 | empty |
| 2 | 103 | 0.56 | 0.84 | 17 | empty |
| 3 | 70 | 0.52 | 0.86 | 19 | empty |
| 4 | 89 | 0.49 | 0.82 | 17 | empty |
| 5 | 67 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- C–F · 454 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 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 O00602
- Elsewhere: RCSB PDB 2JHH · PDBe 2JHH · UniProt O00602
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