Research workbench

L-ficolin complexed to phosphocholine

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

PDB: 4NYT
Type: protein
Length: 640 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ficolin-2
UniProt: Q15485
Ligands: PC, NAG, MAN, FUC, CA, PO4
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Ficolin-2	protein	216	14% helix, 31% strand	Q15485
A, B	Ficolin-2	protein	212	16% helix, 33% strand	Q15485

Ligands and binding sites

PC · Phosphocholine · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, A
MAN · alpha-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains C
CA · Calcium ion · metal · 4 copies · chains C, A, B
PO4 · Phosphate ion · ion · chains C
ACT · Acetate ion · additive · 2 copies · chains C, A

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	800	0.79	0.82	81	empty
2	243	0.68	0.84	35	empty
3	103	0.48	0.81	17	empty
4	84	0.47	0.82	20	empty
5	83	0.45	0.81	16	empty

Interfaces

3 interfaces between chains.

C–B · 571 Å² buried · 8 hydrogen bonds · protein-protein
C–A · 522 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 468 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4NYT · L-Ficolin Complexed to Phosphocholine · the same entry in another collection · chain C against C, TM-score 1.00
Q15485 · AlphaFold monomer V2.0 prediction for ficolin-2 (Q15485) · a predicted model of the same protein · chain A 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 4NYT · PDBe 4NYT · UniProt Q15485

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