MolNFT v1 · #11873 · protein

Crystal structure of a galactose-specific C-type lectin

1JZN · Galactose-specific lectin: “Crystal structure of a galactose-specific C-type lectin”. X-ray diffraction, 5 ligands (BGC, GAL, CA), 9 pockets (best druggability 0.49). MolNFT v1 #11873 on GenesisL1: 3D structure, binding sites and…

PDB: 1JZN
Type: protein
Length: 675 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactose-specific lectin
UniProt: P21963
Ligands: BGC, GAL, CA, NA, CL
Pockets: 9 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Galactose-specific lectin	protein	135	23% helix, 30% strand	P21963

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 5 copies · chains B, D
GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, B, C, D, E
CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
CL · Chloride ion · ion · chains B

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

Pockets

9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	145	0.49	0.79	29	empty
2	129	0.48	0.79	22	empty
3	213	0.47	0.74	42	empty
4	142	0.42	0.75	22	empty
5	93	0.38	0.76	17	empty

Interfaces

5 interfaces between chains.

A–E · 702 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 676 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 673 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 666 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 650 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

1JZN · crystal structure of a galactose-specific C-type lectin · the same entry in another collection · chain A against A, TM-score 1.00
P21963 · AlphaFold monomer V2.0 prediction for C-type lectin cal (P21963) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P21963
Elsewhere: RCSB PDB 1JZN · PDBe 1JZN · UniProt P21963

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