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L-ficolin complexed to N-acetyl-cystein (150MM)

Analyse L-ficolin complexed to N-acetyl-cystein (150MM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2J2P
Type: protein
Length: 1,288 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ficolin-2
UniProt: Q15485
Ligands: SC2, NAG, BMA, CA
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Ficolin-2	protein	214	16% helix, 30% strand	Q15485
B, E	Ficolin-2	protein	218	19% helix, 33% strand	Q15485
C, F	Ficolin-2	protein	212	15% helix, 32% strand	Q15485

Ligands and binding sites

SC2 · N-acetyl-L-cysteine · ligand · 13 copies · chains A, B, C, D, F, E
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, E
BMA · beta-D-mannopyranose · sugar · chains C
CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	521	0.74	0.82	50	SC2
2	292	0.67	0.83	33	SC2
3	279	0.67	0.83	34	SC2
4	274	0.65	0.82	25	SC2
5	244	0.65	0.83	34	SC2

Interfaces

8 interfaces between chains.

A–B · 598 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 544 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 525 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 500 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 488 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

2J2P · L-ficolin complexed to N-acetyl-cystein (150mM) · the same entry in another collection · chain A against A, 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 2J2P · PDBe 2J2P · UniProt Q15485

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