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Crystal structure of variable lymphocyte receptor (vlr) RBC36 in complex with H-trisaccharide

Analyse Crystal structure of variable lymphocyte receptor (vlr) RBC36 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3E6J
Type: protein
Length: 219 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Variable lymphocyte receptor diversity region
Ligands: NAG, GAL, FUC, SO4
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Variable lymphocyte receptor diversity region	protein	219	11% helix, 17% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
GAL · beta-D-galactopyranose · sugar · chains A
FUC · alpha-L-fucopyranose · sugar · chains A
SO4 · Sulfate ion · ion · 5 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	67	0.31	0.74	15	GAL

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3E6J · Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with… · the same entry in another collection · 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
Elsewhere: RCSB PDB 3E6J · PDBe 3E6J

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