MolNFT v1 · #113564 · protein

X-ray structure of the rsl lectin in complex with lewis X tetrasaccahride

5AJB: “X-ray structure of the rsl lectin in complex with lewis X tetrasaccahride”. X-ray diffraction, 4 ligands (NAG, FUC, GAL), 1 pocket (best druggability 0.75). MolNFT v1 #113564 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5AJB
Type: protein
Length: 267 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: D8NA05
Ligands: NAG, FUC, GAL, GLA
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 67% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lectin	protein	89	0% helix, 67% strand	D8NA05
C	Lectin	protein	89	0% helix, 67% strand	D8NA05

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B, C
GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, B, C
GLA · alpha-D-galactopyranose · sugar

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	622	0.75	0.81	62	empty

Interfaces

3 interfaces between chains.

A–B · 801 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 794 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 751 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5AJB · X-ray structure of the RSL lectin in complex with Lewis X tetrasaccahride · 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
Every structure of UniProt D8NA05
Elsewhere: RCSB PDB 5AJB · PDBe 5AJB · UniProt D8NA05

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