Research workbench
L-ficolin complexed to galactose
Analyse L-ficolin complexed to galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J3U
- Type
- protein
- Length
- 1,300 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ficolin-2
- UniProt
- Q15485
- Ligands
- NAG, GLA, MAN, CA
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Ficolin-2 | protein | 217 | 14% helix, 33% strand | Q15485 |
| B, E | Ficolin-2 | protein | 218 | 16% helix, 33% strand | Q15485 |
| C | Ficolin-2 | protein | 214 | 15% helix, 34% strand | Q15485 |
| D | Ficolin-2 | protein | 216 | 14% helix, 32% strand | Q15485 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, E, C, F
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains B, C, E, F
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 5 copies · chains B, F, C, E
- P4C · O-acetaldehydyl-hexaethylene glycol · additive · 5 copies · chains A, B, C, D, E, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.83 | 0.84 | 109 | P4C, GLA |
| 2 | 1163 | 0.82 | 0.83 | 128 | P4C, GLA |
| 3 | 76 | 0.48 | 0.83 | 18 | empty |
| 4 | 130 | 0.48 | 0.78 | 23 | empty |
| 5 | 90 | 0.46 | 0.81 | 18 | empty |
Interfaces
8 interfaces between chains.
- D–E · 581 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 529 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 504 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 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 2J3U · PDBe 2J3U · UniProt Q15485
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