MolNFT v1 · #144844 · protein

Structure of glycolipid AGSA[26,6P] in complex with mouse CD1D

6C6E: “Structure of glycolipid AGSA[26,6P] in complex with mouse CD1D”. X-ray diffraction, 3 ligands (EM4, NAG, NA). MolNFT v1 #144844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C6E
Type: protein
Length: 368 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: A0A0R4J090, P01887
Ligands: EM4, NAG, NA

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	272	—	A0A0R4J090
B	—	protein	96	—	P01887

Ligands and binding sites

EM4 · N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl) amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]hexacosanamide · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
NA · Sodium ion · metal · 2 copies · chains A

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

Compared structures

6C6E · Structure of glycolipid aGSA[26,6P] 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 0.98

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 A0A0R4J090
Every structure of UniProt P01887
Elsewhere: RCSB PDB 6C6E · PDBe 6C6E · UniProt A0A0R4J090 · UniProt P01887

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