MolNFT v1 · #40782 · protein

L-ficolin complexed to N-acetyl-D-glucosamine

2J3O · Ficolin-2: “L-ficolin complexed to N-acetyl-D-glucosamine”. X-ray diffraction, 2 ligands (NAG, CA), 15 pockets (best druggability 0.80). MolNFT v1 #40782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2J3O
Type: protein
Length: 1,302 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ficolin-2
UniProt: Q15485
Ligands: NAG, CA
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, F	Ficolin-2	protein	217	14% helix, 30% strand	Q15485
B	Ficolin-2	protein	218	17% helix, 32% strand	Q15485
D	Ficolin-2	protein	216	16% helix, 32% strand	Q15485

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, F, E
CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

15 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	811	0.80	0.83	77	NAG
2	1100	0.80	0.81	103	NAG
3	307	0.69	0.83	42	NAG
4	335	0.63	0.79	30	NAG
5	94	0.49	0.82	24	empty

Interfaces

6 interfaces between chains.

A–C · 557 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 522 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 513 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 497 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 479 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

2J3O · L-ficolin complexed to N-acetyl-D-glucosamine · 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 C 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 2J3O · PDBe 2J3O · UniProt Q15485

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