4ZAK

Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A (A)	Antigen-presenting glycoprotein CD1d1	polymer	285	32632.7	1	UniProt (P11609) Pfam (PF16497) Pfam (PF07654)	Mus musculus (Mouse)
2	B (B)	Beta-2-microglobulin	polymer	99	11660.4	1	UniProt (P01887) Pfam (PF07654)	Mus musculus (Mouse)
3	C (C)	Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain	polymer	209	23055.6	1	UniProt (A0A0B4J1J9) UniProt (A0N4Z0) UniProt (K7N5M3) Pfam (PF07686) Pfam (PF09291) UniProt (by SIFTS) (A0A0G2JG46)	Mus musculus (Mouse)	Protein Trav11d,Human nkt tcr beta chain
4	D (D)	T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region	polymer	241	27027.0	1	UniProt (A0A075B5J4) UniProt (A0A5B9) Pfam (PF07686) Pfam (PF07654) UniProt (by SIFTS) (A2NTY6) UniProt (by SIFTS) (A0N8J3)	Mus musculus
5	E (E)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	1	In PDB GlyTouCan (G42666HT)
6	F, G (A)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	2	Chemie (NAG)
7	H (A)	N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide	non-polymer		874.4	1	Chemie (4LX)

Sequence modifications

A: 1 - 279 (UniProt: P11609)

PDB	External Database	Details
His 201	Asp 219	conflict
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

C: 94 - 112 (UniProt: A0N4Z0)

PDB	External Database	Details
Ala 98	Thr 6	conflict
His 103	Tyr 11	conflict
Ala 106	Arg 14	conflict
Ile 111	Thr 19	conflict
Ile 113	-	linker

C: 114 - 208 (UniProt: K7N5M3)
D: 0 - 112 (PDB: 4ZAK)
D: 113 - 129 (UniProt: A0A075B5J4)
D: 130 - 240 (UniProt: A0A5B9)

PDB	External Database	Details
Cys 168	Ser 56	engineered mutation
Ser 186	Cys 74	engineered mutation

Contents of the asymmetric unit

Polymers	Number of chains	4
	Total formula weight	94375.6
Branched	Number of molecules	1
	Total formula weight	424.4
Non-Polymers*	Number of molecules	3
	Total formula weight	1316.8
All*	Total formula weight	96116.8

*Water molecules are not included.