2YP6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PNEUMOCCOCAL EXPOSED LIPOPROTEIN THIOREDOXIN SP_1000 (ETRX2) FROM STREPTOCOCCUS PNEUMONIAE STRAIN TIGR4 IN COMPLEX WITH CYCLOFOS 3 TM

Authors :   S. G. Bartual, M. Shalek, M. R. Abdullah, I. Jensch, T. M. Asmat, L. Petru T. Pribyl, J. A. Hermoso, S. Hammerschmidt

Date :   29 Oct 12 (Deposition) - 30 Oct 13 (Release) - 11 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Saleh, S. G. Bartual, M. R. Abdullah, I. Jensch, T. M. Asmat, L. Petruschka, T. Pribyl, M. Gellert, C. H. Lillig, H. Antelmann, J. A. Hermoso, S. Hammerschmidt
Molecular Architecture Of Streptococcus Pneumoniae Surface Thioredoxin-Fold Lipoproteins Crucial For Extracellular Oxidative Stress Resistance And Maintenance Of Virulence.
Embo Mol. Med. V. 5 1852 2013
PubMed-ID: 24136784 | Reference-DOI: 10.1002/EMMM.201202435

Molecule 1 - THIOREDOXIN FAMILY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE TIGR4
	Organism Taxid	:	170187

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	C6W	4	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLPHOSPHOCHOLINE
2	MLI	8	Ligand/Ion	MALONATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	C6W	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLPHOSPHOCHOLINE
2	MLI	2	Ligand/Ion	MALONATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	C6W	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLPHOSPHOCHOLINE
2	MLI	2	Ligand/Ion	MALONATE ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	C6W	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLPHOSPHOCHOLINE
2	MLI	2	Ligand/Ion	MALONATE ION

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	C6W	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLPHOSPHOCHOLINE
2	MLI	2	Ligand/Ion	MALONATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP B:80 , GLN B:113	BINDING SITE FOR RESIDUE C6W B1186
02	AC2	SOFTWARE	TRP A:80 , GLN A:113	BINDING SITE FOR RESIDUE C6W A1186
03	AC3	SOFTWARE	GLN C:113 , PHE C:144	BINDING SITE FOR RESIDUE C6W C1186
04	AC4	SOFTWARE	PRO A:83 , ILE A:152 , PRO A:153 , GLY A:170 , HOH A:2109	BINDING SITE FOR RESIDUE MLI A1187
05	AC5	SOFTWARE	SER B:79 , LYS B:85 , LYS B:116 , TRP B:124 , HOH B:2102	BINDING SITE FOR RESIDUE MLI B1187
06	AC6	SOFTWARE	GLN D:113 , GLY D:114 , PHE D:144	BINDING SITE FOR RESIDUE C6W D1186
07	AC7	SOFTWARE	ARG C:100 , GLU C:103 , ILE C:104 , PRO C:134 , HOH C:2078	BINDING SITE FOR RESIDUE MLI C1187
08	AC8	SOFTWARE	ASP D:58 , MLI D:1188 , HOH D:2016 , HOH D:2085	BINDING SITE FOR RESIDUE MLI D1187
09	AC9	SOFTWARE	ARG D:100 , GLU D:103 , ILE D:104 , PRO D:134 , MLI D:1187 , HOH D:2028 , HOH D:2059 , HOH D:2086 , HOH D:2087	BINDING SITE FOR RESIDUE MLI D1188
10	BC1	SOFTWARE	ARG A:100 , GLU A:103 , ILE A:104 , PRO A:134 , HOH A:2086	BINDING SITE FOR RESIDUE MLI A1188
11	BC2	SOFTWARE	ARG B:100 , GLU B:103 , ILE B:104 , PRO B:134 , HOH B:2052 , HOH B:2065 , HOH B:2103	BINDING SITE FOR RESIDUE MLI B1188
12	BC3	SOFTWARE	LYS C:85 , LYS C:116 , TRP C:124 , HOH C:2047 , HOH C:2114	BINDING SITE FOR RESIDUE MLI C1188

Asymmetric Unit

No.	Residues
1	A:81	-	A:84
2	B:81	-	B:84
3	C:81	-	C:84
4	D:81	-	D:84

Asymmetric Unit

No.	Residues
1	Ile A:152	-	Pro A:153
2	Ile B:152	-	Pro B:153
3	Ile C:152	-	Pro C:153
4	Ile D:152	-	Pro D:153

(no "SAP(SNP)/Variant" information available for 2YP6)

(no "PROSITE Motif" information available for 2YP6)

(no "Exon" information available for 2YP6)

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:143
 aligned with A0A0H2UPR5_S | A0A0H2UPR5 from UniProtKB/TrEMBL  Length:185

    Alignment length:143
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182   
         A0A0H2UPR5_S    43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
               SCOP domains d2yp6a_ A: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee....eee.hhhh..eeeeee....hhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh......eee...hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yp6 A  43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:143
 aligned with A0A0H2UPR5_S | A0A0H2UPR5 from UniProtKB/TrEMBL  Length:185

    Alignment length:143
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182   
         A0A0H2UPR5_S    43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
               SCOP domains d2yp6b_ B: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee....eee.hhhh..eeeeee....hhhhhhhhhhhhhhhh.....eeeeeee..........hhhhhhhhhh......eee...hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yp6 B  43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain C from PDB  Type:PROTEIN  Length:143
 aligned with A0A0H2UPR5_S | A0A0H2UPR5 from UniProtKB/TrEMBL  Length:185

    Alignment length:143
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182   
         A0A0H2UPR5_S    43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
               SCOP domains d2yp6c_ C: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.....eee.hhhh..eeeeee....hhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh......eee...hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yp6 C  43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain D from PDB  Type:PROTEIN  Length:143
 aligned with A0A0H2UPR5_S | A0A0H2UPR5 from UniProtKB/TrEMBL  Length:185

    Alignment length:143
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182   
         A0A0H2UPR5_S    43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
               SCOP domains d2yp6d_ D: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee....eee.hhhh..eeeeee....hhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhh......eee...hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yp6 D  43 IAVGKDAPDFTLQSMDGKEVKLSDFKGKKVYLKFWASWCGPCKKSMPELMELAAKPDRDFEILTVIAPGIQGEKTVEQFPQWFQEQGYKDIPVLYDTKATTFQAYQIRSIPTEYLIDSQGKIGKIQFGAISNADAEAAFKEMN 185
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182

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: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: automated matches (347)

Protein domain: automated matches (347)

Streptococcus pneumoniae [TaxId: 170187] (3)

1a	d2yp6a_	A:
1b	d2yp6b_	B:
1c	d2yp6c_	C:
1d	d2yp6d_	D:

(no "CATH Domain" information available for 2YP6)

(no "Pfam Domain" information available for 2YP6)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2YP6)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		C6W	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MLI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:152 - Pro A:153	[ RasMol ]
		Ile B:152 - Pro B:153	[ RasMol ]
		Ile C:152 - Pro C:153	[ RasMol ]
		Ile D:152 - Pro D:153	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2yp6
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A0A0H2UPR5_S \| A0A0H2UPR5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	A0A0H2UPR5_S \| A0A0H2UPR5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	A0A0H2UPR5_S \| A0A0H2UPR5	:	4hqz

(no "Related Entries Specified in the PDB File" available for 2YP6)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File