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Structure of alpha-GSA[20,6P] bound by CD1D and in complex with the VA14VB8.2 TCR

Analyse Structure of alpha-GSA[20,6P] bound by CD1D and in complex with the VA14VB8.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CXA
Type: protein
Length: 805 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: A0A0R4J090, P01887
Ligands: EMG, NAG, BMA, MAN, FUC, NA

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	266	—	A0A0R4J090
B	—	protein	98	—	P01887
C	—	protein	202	—	—
D	—	protein	239	—	—

Ligands and binding sites

EMG · 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]icosanamide · ligand · chains A, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains A
NA · Sodium ion · metal · 4 copies · chains A, C, D

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

Compared structures

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

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Elsewhere: RCSB PDB 6CXA · PDBe 6CXA · UniProt A0A0R4J090 · UniProt P01887

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