MolNFT v1 · #40788 · protein

L-ficolin complexed to galactose

2J3U · Ficolin-2: “L-ficolin complexed to galactose”. X-ray diffraction, 4 ligands (NAG, GLA, MAN), 17 pockets (best druggability 0.83). MolNFT v1 #40788 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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.

Pocket	Volume (Å³)	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 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 580 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 529 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 527 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 504 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

2J3U · L-ficolin complexed to galactose · 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 E 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 2J3U · PDBe 2J3U · UniProt Q15485

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