MolNFT v1 · #144820 · protein

Structure of glycolipid AGSA[8,9] in complex with mouse CD1D

6C5M: “Structure of glycolipid AGSA[8,9] in complex with mouse CD1D”. X-ray diffraction, 6 ligands (J81, PLM, NAG). MolNFT v1 #144820 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C5M
Type: protein
Length: 365 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: A0A0R4J090, P01887
Ligands: J81, PLM, NAG, MAN, BMA, FUC

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	267	—	A0A0R4J090
B	—	protein	98	—	P01887

Ligands and binding sites

J81 · (5R,6S,7S)-5,6-dihydroxy-N-nonyl-7-(octanoylamino)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl) tetrahydro-2H-pyran-2-yl]oxy}octanamide (non-preferred name) · ligand · chains A
PLM · Palmitic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies
BMA · beta-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains A

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

Compared structures

6C5M · Structure of glycolipid aGSA[8,9] in complex with mouse CD1d · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 A0A0R4J090
Every structure of UniProt P01887
Elsewhere: RCSB PDB 6C5M · PDBe 6C5M · UniProt A0A0R4J090 · UniProt P01887

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