2APT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN

Authors :   S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M R. A. Mariuzza, E. J. Sundberg

Date :   16 Aug 05 (Deposition) - 21 Mar 06 (Release) - 29 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   The Murine T Cell Receptor V Beta 8. 2 Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Cho, C. P. Swaminathan, J. Yang, M. C. Kerzic, R. Guan, M. C. Kieke, D. M. Kranz, R. A. Mariuzza, E. J. Sundberg
Structural Basis Of Affinity Maturation And Intramolecular Cooperativity In A Protein-Protein Interaction.
Structure V. 13 1775 2005
PubMed-ID: 16338399 | Reference-DOI: 10.1016/J.STR.2005.08.015

Molecule 1 - T-CELL RECEPTOR BETA CHAIN V
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MLA	1	Ligand/Ion	MALONIC ACID

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MLA	-1	Ligand/Ion	MALONIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MLA	1	Ligand/Ion	MALONIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:8 , ASN A:10 , PRO B:8 , ARG B:9 , ASN B:10 , HOH B:243 , HOH B:244	BINDING SITE FOR RESIDUE MLA B 200

Asymmetric Unit

No.	Residues
1	A:23	-	A:92
2	B:23	-	B:92

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Ser B:7	-	Pro B:8

(no "SAP(SNP)/Variant" information available for 2APT)

(no "PROSITE Motif" information available for 2APT)

(no "Exon" information available for 2APT)

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:109
 aligned with A2NAI0_RAT | A2NAI0 from UniProtKB/TrEMBL  Length:95

    Alignment length:109
                                                                                                                       95                
                                    12        22        32        42        52        62        72        82        92  |      -         
           A2NAI0_RAT     3 AAVTQSPRNKVTVTGKNVTFNCHQTDNHNYMYWYRQDMGHGLRLIHYSYGSGSFENGDIPEGYKVSRPNQENFFLTLESASPSQTSVYFCASS----------------   -
               SCOP domains d2apta_ A: automated matches                                                                                  SCOP domains
               CATH domains 2aptA00 A:2-117 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eeee.....eeeeee...hhhhheeeeeeeee..eeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2apt A   2 AAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGNTEKGDIPDGYEASRPSHEQFSLILVSATPSQSSVYFCASGVGGTLYFGAGTRLSVL 117
                                    11        21        31        41        51        61 ||     72        82        92       108         
                                                                                        63|                                 101|         
                                                                                         65                                  108

Chain A from PDB  Type:PROTEIN  Length:109
 aligned with TVB5_MOUSE | P04213 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:113
                                    19        29        39        49        59        69        79        89        99       109       119   
           TVB5_MOUSE    10 AAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSGTGGALDTQYFGPGTRLLVL 122
               SCOP domains d2apta_ A: automated matches                                                                                      SCOP domains
               CATH domains 2aptA00 A:2-117 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eeee.....eeeeee...hhhhheeeeeee-ee..eee---e...eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2apt A   2 AAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGNTEKGDIPDGYEASRPSHEQFSLILVSATPSQSSVYFCAS-GVGGTLY---FGAGTRLSVL 117
                                    11        21        31        41        51        61 ||     72        82        92 | |   101   |   114   
                                                                                        63|                           94 |   101 108         
                                                                                         65                             95

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with A2NAI0_RAT | A2NAI0 from UniProtKB/TrEMBL  Length:95

    Alignment length:109
                                                                                                                       95                
                                    12        22        32        42        52        62        72        82        92  |      -         
           A2NAI0_RAT     3 AAVTQSPRNKVTVTGKNVTFNCHQTDNHNYMYWYRQDMGHGLRLIHYSYGSGSFENGDIPEGYKVSRPNQENFFLTLESASPSQTSVYFCASS----------------   -
               SCOP domains d2aptb_ B: automated matches                                                                                  SCOP domains
               CATH domains 2aptB00 B:2-117 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eeeeeee..eeeeee...hhhhheeeeeeee.....ee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2apt B   2 AAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGNTEKGDIPDGYEASRPSHEQFSLILVSATPSQSSVYFCASGVGGTLYFGAGTRLSVL 117
                                    11        21        31        41        51        61 ||     72        82        92       108         
                                                                                        63|                                 101|         
                                                                                         65                                  108

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with TVB5_MOUSE | P04213 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:113
                                    19        29        39        49        59        69        79        89        99       109       119   
           TVB5_MOUSE    10 AAVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSGTGGALDTQYFGPGTRLLVL 122
               SCOP domains d2aptb_ B: automated matches                                                                                      SCOP domains
               CATH domains 2aptB00 B:2-117 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee......eeeeeee..eeeeee...hhhhheeeeeee-e.....e---e...eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2apt B   2 AAVTQSPRNKVAVTGEKVTLSCQQTNNHNNMYWYRQDTGHGLRLIHYSYGAGNTEKGDIPDGYEASRPSHEQFSLILVSATPSQSSVYFCAS-GVGGTLY---FGAGTRLSVL 117
                                    11        21        31        41        51        61 ||     72        82        92 | |   101   |   114   
                                                                                        63|                           94 |   101 108         
                                                                                         65                             95

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: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Norway rat (Rattus norvegicus) [TaxId: 10116] (7)

1a	d2apta_	A:
1b	d2aptb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Norway rat (Rattus norvegicus) (32)

1a	2aptA00	A:2-117
1b	2aptB00	B:2-117

(no "Pfam Domain" information available for 2APT)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2APT)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		MLA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
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	TVB5_MOUSE \| P04213
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		Domain Information	:	XDom
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TVB5_MOUSE \| P04213	:	1d9k 1lp9 1u3h 2apb 2apf 2apv 2apw 2apx 2aq1 2aq2 2aq3 2icw 2j8u 2uwe 4nhu
UniProtKB/TrEMBL
	A2NAI0_RAT \| A2NAI0	:	2apb 2apf 2apv 2apw 2apx

2apb	THE G17E/S54N/L81S VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apf	THE G17E/A52V/S54N/K66E/L81S VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apv	THE G17E/A52V/S54N/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apw	THE G17E/A52V/S54N/K66E/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2apx	THE G17E/A52V/S54N/K66E/Q72H/E80V/L81S/T87S/G96V VARIANT OF THE MURINE T CELL RECEPTOR V BETA 8.2 DOMAIN
2aq1	T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/A52V/S54N/K66E/ E80V/L81S/T87S/G96V) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT
2aq2	T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/A52V/S54N/K66E/ L81S) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT
2aq3	T-CELL RECEPTOR V BETA DOMAIN VARIANT (G17E/L81S) COMPLEXED WITH SUPERANTIGEN SEC3 MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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Related Entries Specified in the PDB File