3TYF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A CD1D-LYSOPHOSPHATIDYLCHOLINE REACTIVE INKT TCR

Authors :   J. Lopez-Sagaseta, E. J. Adams

Date :   24 Sep 11 (Deposition) - 25 Apr 12 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.81

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Immunoglobulin-Like, Antigen Recognition, Cd1D, Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lopez-Sagaseta, L. V. Sibener, J. E. Kung, J. Gumperz, E. J. Adams
Lysophospholipid Presentation By Cd1D And Recognition By A Human Natural Killer T-Cell Receptor.
Embo J. V. 31 2047 2012
PubMed-ID: 22395072 | Reference-DOI: 10.1038/EMBOJ.2012.54

Molecule 1 - INKT CELL RECEPTOR ALPHA CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - INKT CELL RECEPTOR BETA CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	GOL	9	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:180 , LYS A:181	BINDING SITE FOR RESIDUE GOL A 301
2	AC2	SOFTWARE	GLY A:106 , GLN C:144	BINDING SITE FOR RESIDUE GOL A 302
3	AC3	SOFTWARE	PRO A:118 , ASP A:198	BINDING SITE FOR RESIDUE GOL A 303
4	AC4	SOFTWARE	GLN B:36 , ASP B:38 , SER B:84 , THR B:86	BINDING SITE FOR RESIDUE GOL B 301
5	AC5	SOFTWARE	GLU B:132 , GLU B:241 , GLU D:222	BINDING SITE FOR RESIDUE GOL B 302
6	AC6	SOFTWARE	GLU C:197	BINDING SITE FOR RESIDUE GOL C 301
7	AC7	SOFTWARE	PHE C:190 , ASN C:191 , SER C:193	BINDING SITE FOR RESIDUE GOL C 302
8	AC8	SOFTWARE	GLU B:222 , SER C:128 , GLU D:132	BINDING SITE FOR RESIDUE GOL C 303
9	AC9	SOFTWARE	GLU A:197 , GLN D:36 , ASP D:38 , SER D:84 , THR D:86 , SER D:87	BINDING SITE FOR RESIDUE GOL D 1000

Asymmetric Unit

No.	Residues
1	A:22	-	A:89
2	A:136	-	A:186
3	A:161	-	B:174
4	B:23	-	B:91
5	B:148	-	B:213
6	C:22	-	C:89
7	C:136	-	C:186
8	C:161	-	D:174
9	D:23	-	D:91
10	D:148	-	D:213

Asymmetric Unit

No.	Residues
1	Ser A:6	-	Pro A:7
2	Ser A:27	-	Pro A:28
3	Asp A:152	-	Ser A:153
4	Ser A:193	-	Ile A:194
5	Thr B:7	-	Pro B:8
6	Tyr B:154	-	Pro B:155
7	Ser C:6	-	Pro C:7
8	Ser C:27	-	Pro C:28
9	Thr D:7	-	Pro D:8
10	Tyr D:154	-	Pro D:155

(no "SAP(SNP)/Variant" information available for 3TYF)

(no "PROSITE Motif" information available for 3TYF)

(no "Exon" information available for 3TYF)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d3tyfa1 A:1-114 automated matches                                                                                 d3tyfa2 A:115-202 automated matches                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee....eeeeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee.......eee...eeeeee........eeeee......eeeeee................ee...eeeee....eeeeeeeeee....hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tyf A   1 NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKDFACANAFNNSIIPEDTFFP 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|      142       152       162       172       183       193         
                                                                                                                                                           130|                                             181|                   
                                                                                                                                                            133                                              183

Chain B from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains d3tyfb1 B:3-118 automated matches                                                                              d3tyfb2 B:119-247 automated matches                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee......eeeeee......eeeeee.............ee.........eee...hhhhheeeeeeee........eee...eeeeee.........eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..ee....eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tyf B   3 DIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTKGDLSESTVSRIRTEHFPLTLESARPSHTSQYLCASSEEGALVGTQYFGPGTRLLVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    12        22        32        42        52  ||   |64        74        84        94    || 107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
                                                                               55|  61|                                  99|                                                                                                                                                
                                                                                57   63                                  103

Chain C from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains d3tyfc1 C:1-114 automated matches                                                                                d3tyfc2 C:115-202 automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee....eeeeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee.....eeee...eeeeee........eeeeeee....eeeeee..............eee...eeeee....eeeeeeeeee...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tyf C   1 NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSKSVCLFTDFDSQTNVSQSDSDVYITDKCVLDMRSMDFKSNSAVAWSNSDFACANAFNNSIIPEDTFFP 202
                                    10        20        30        40        50        60        70        80        90     ||101       111       121       133       143      |154       164       174     ||185       195       
                                                                                                                          96|                             130|              150|                         180|                    
                                                                                                                           98                              133               152                          182

Chain D from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains d3tyfd1 D:3-118 automated matches                                                                                d3tyfd2 D:119-247 automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeee......eeeeee......ee......ee.........eee.........eeeeeee....................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tyf D   3 DIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSEEGALKEGTQYFGPGTRLLVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    12        22        32        42        52     || 63        73        83        93       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245  
                                                                                  58|                                      101|                                                                                                                                               
                                                                                   60                                       104

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Escherichia coli [TaxId: 562] (1)

1a	d3tyfa1	A:1-114
1b	d3tyfb1	B:3-118
1c	d3tyfc1	C:1-114
1d	d3tyfd1	D:3-118

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Escherichia coli [TaxId: 562] (1)

2a	d3tyfa2	A:115-202
2b	d3tyfb2	B:119-247
2c	d3tyfc2	C:115-202
2d	d3tyfd2	D:119-247

(no "CATH Domain" information available for 3TYF)

(no "Pfam Domain" information available for 3TYF)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3TYF)

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:152 - Ser A:153	[ RasMol ]
		Ser A:193 - Ile A:194	[ RasMol ]
		Ser A:27 - Pro A:28	[ RasMol ]
		Ser A:6 - Pro A:7	[ RasMol ]
		Ser C:27 - Pro C:28	[ RasMol ]
		Ser C:6 - Pro C:7	[ RasMol ]
		Thr B:7 - Pro B:8	[ RasMol ]
		Thr D:7 - Pro D:8	[ RasMol ]
		Tyr B:154 - Pro B:155	[ RasMol ]
		Tyr D:154 - Pro D:155	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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	3tyf
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Sites (9, 9)

SS Bonds (10, 10)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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