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L-FICOLIN

Analyse L-FICOLIN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2J3G
Type: protein
Length: 1,292 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ficolin-2
UniProt: Q15485
Ligands: NAG, BMA, MAN, FUC, CA
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 16% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Ficolin-2	protein	213	16% helix, 33% strand	Q15485
B, D	Ficolin-2	protein	217	15% helix, 33% strand	Q15485
E	Ficolin-2	protein	218	17% helix, 33% strand	Q15485
F	Ficolin-2	protein	214	15% helix, 33% strand	Q15485

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, E
BMA · beta-D-mannopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains B
CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
P4C · O-acetaldehydyl-hexaethylene glycol · additive · chains D, E

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1137	0.79	0.81	111	empty
2	1196	0.78	0.80	116	P4C
3	507	0.69	0.79	54	empty
4	242	0.55	0.77	24	empty
5	119	0.50	0.80	17	empty

Interfaces

6 interfaces between chains.

D–F · 553 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 532 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 520 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 519 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 503 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

2J3G · L-ficolin · the same entry in another collection · chain F against F, TM-score 1.00
Q15485 · AlphaFold monomer V2.0 prediction for ficolin-2 (Q15485) · a predicted model of the same protein · chain F 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 2J3G · PDBe 2J3G · UniProt Q15485

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