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H-ficolin complexed to galactose

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

PDB: 2J5Z
Type: protein
Length: 636 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ficolin-3
UniProt: O75636
Ligands: GAL, CA
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ficolin-3	protein	214	16% helix, 27% strand	O75636
B, C	Ficolin-3	protein	211	16% helix, 30% strand	O75636

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · chains A
CA · Calcium ion · metal · 3 copies · chains A, B, C
ACT · Acetate ion · additive · chains A

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

Pockets

3 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	807	0.74	0.79	76	empty
2	231	0.51	0.76	26	empty
3	164	0.46	0.76	22	empty

Interfaces

3 interfaces between chains.

A–B · 518 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 447 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 416 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

2J5Z · H-ficolin complexed to galactose · the same entry in another collection · chain A against A, TM-score 1.00
O75636 · AlphaFold monomer V2.0 prediction for ficolin-3 (O75636) · 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 O75636
Elsewhere: RCSB PDB 2J5Z · PDBe 2J5Z · UniProt O75636

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