5VCJ

Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	Antigen-presenting glycoprotein CD1d1	polymer	285	32632.7	1	UniProt (P11609) Pfam (PF16497) Pfam (PF07654) In PDB	Mus musculus (Mouse)
2	B	Beta-2-microglobulin	polymer	99	11660.4	1	UniProt (P01887) Pfam (PF07654) In PDB	Mus musculus (Mouse)
3	C	Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)	polymer	209	23055.6	1	UniProt (A0A0B4J1J9) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291) In PDB	Mus musculus (Mouse)	T cell receptor alpha variable 11D,Human nkt tcr beta chain
4	D	Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)	polymer	241	27027.0	1		Mus musculus (Mouse)
5	E	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	branched		1057.0	1	In PDB GlyTouCan (G82348BZ)
6	A	(2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside	non-polymer		479.6	1	Chemie (N57)
7	A	PALMITIC ACID	non-polymer		256.4	1	Chemie (PLM)
8	A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	2	Chemie (NAG)

Sequence modifications

A: 1 - 279 (UniProt: P11609)

PDB	External Database	Details
His 201	Asp 219	engineered mutation
His 280	-	expression tag
His 281	-	expression tag
His 282	-	expression tag
His 283	-	expression tag
His 284	-	expression tag
His 285	-	expression tag

C: 1 - 93 (UniProt: A0A0B4J1J9)

PDB	External Database	Details
Met 0	-	initiating methionine
Asp 94	-	linker
Arg 95	-	linker
Gly 96	-	linker
Ser 97	-	linker
Ala 98	-	linker
Leu 99	-	linker
Gly 100	-	linker
Arg 101	-	linker
Leu 102	-	linker
His 103	-	linker
Phe 104	-	linker
Gly 105	-	linker
Ala 106	-	linker
Gly 107	-	linker
Thr 108	-	linker
Gln 109	-	linker
Leu 110	-	linker
Ile 111	-	linker
Val 112	-	linker
Ile 113	-	linker

C: 114 - 208 (UniProt: K7N5M3)
D: 0 - 129 (PDB: 5VCJ)
D: 130 - 240 (PDB: 5VCJ)

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	94375.6
Branched	Number of molecules	1
	Total formula weight	1057.0
Non-Polymers*	Number of molecules	4
	Total formula weight	1178.5
All*	Total formula weight	96611.1

*Water molecules are not included.