Research workbench

L-ficolin complexed to glucosamine-6-sulfate

Analyse L-ficolin complexed to glucosamine-6-sulfate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R9J
Type: protein
Length: 651 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ficolin-2
UniProt: Q15485
Ligands: 3LJ, NAG, BMA, CA, SO4
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, A, B	Ficolin-2	protein	217	14% helix, 34% strand	Q15485

Ligands and binding sites

3LJ · 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose · ligand · 3 copies · chains A, B, G
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains G, A
BMA · beta-D-mannopyranose · sugar
CA · Calcium ion · metal · 4 copies · chains G, A, B
SO4 · Sulfate ion · ion · chains G
ACT · Acetate ion · additive · 7 copies · chains G, A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	782	0.78	0.82	83	ACT
2	294	0.67	0.83	34	empty
3	87	0.52	0.84	19	empty
4	67	0.48	0.84	17	empty
5	96	0.47	0.80	17	empty

Interfaces

3 interfaces between chains.

G–B · 556 Å² buried · 8 hydrogen bonds · protein-protein
G–A · 520 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 412 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4R9J · L-ficolin complexed to glucosamine-6-sulfate · the same entry in another collection · chain G against G, TM-score 1.00
Q15485 · AlphaFold monomer V2.0 prediction for ficolin-2 (Q15485) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 4R9J · PDBe 4R9J · UniProt Q15485

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