6V80

Crystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, F (A, F)	Antigen-presenting glycoprotein CD1d	polymer	347	39471.6	2	UniProt (P15813) Pfam (PF16497) Pfam (PF07654)	Homo sapiens (Human)	R3G1
2	B, G (B, G)	Beta-2-microglobulin	polymer	100	11879.4	2	UniProt (P61769) Pfam (PF07654)	Homo sapiens (Human)
3	C, H (C, H)	T cell receptor alpha variable 10, nkt tcr alpha chain fusion	polymer	210	23365.8	2	UniProt (A0A0B4J240) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291)	Homo sapiens (Human)
4	D, I (D, I)	nkt tcr beta chain	polymer	241	27491.5	2	UniProt (K7N5M4) Pfam (PF07686) Pfam (PF07654)	Homo sapiens (Human)
5	E, J (E, J)	Nanobody VHH ID12	polymer	119	12901.4	2		Lama glama (llama)
6	K, L (K, L)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	2	In PDB GlyTouCan (G42666HT)
7	M, N (A, F)	N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE	non-polymer		858.3	2	Chemie (AGH)
8	O, P (F)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	2	Chemie (NAG)

Sequence modifications

A, F: 5 - 278 (UniProt: P15813)

PDB	External Database	Details
Met 4	-	initiating methionine

A, F: 279 - 350 (PDB: 6V80)
B, G: 1 - 99 (UniProt: P61769)

PDB	External Database	Details
Met 0	-	initiating methionine

C, H: 3 - 95 (UniProt: A0A0B4J240)

PDB	External Database	Details
His 1	-	expression tag
Met 2	-	expression tag

C, H: 96 - 210 (UniProt: K7N5M3)
D, I: 1 - 241 (UniProt: K7N5M4)

Sequence viewer

Contents of the asymmetric unit

*Water molecules are not included.