2OBK - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF THE PUTATIVE SE BINDING PROTEIN FROM PSEUDOMONAS FLUORESCENS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET PLR6.

Authors :   A. P. Kuzin, M. Su, J. Seetharaman, C. X. Chen, Y. Fang, K. Cunningham, L. R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, L. To J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   19 Dec 06 (Deposition) - 02 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   X-Ray Nesg Plr6 Q4Kgc5, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Kuzin, M. Su, J. Seetharaman, C. Chen, Y. Fang, K. Cunningham, L. C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
X-Ray Structure Of The Putative Se Binding Protein From Pseudomonas Fluorescens
To Be Published
PubMed: search

Molecule 1 - SELT/SELW/SELH SELENOPROTEIN DOMAIN
	Atcc	:	BAA-477
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PFL_1582
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	220664
	Strain	:	PF-5

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2OBK)

(no "Site" information available for 2OBK)

Asymmetric Unit

No.	Residues
1	A:13	-	A:16
2	B:13	-	B:16
3	C:13	-	C:16
4	D:13	-	D:16
5	E:13	-	E:16
6	F:13	-	F:16
7	G:13	-	G:16
8	H:13	-	H:16

(no "Cis Peptide Bond" information available for 2OBK)

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

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

(no "Exon" information available for 2OBK)

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:84
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:84
                                    13        23        33        43        53        63        73        83    
          Q4KGC5_PSEF5    4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
               SCOP domains d2obka_ A: automated matches                                                         SCOP domains
               CATH domains 2obkA00 A:4-87 Glutaredoxin                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhhhh.....eeeeeee....eeeee..eeeeehhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2obk A  4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
                                    13        23        33        43        53        63        73        83

Chain B from PDB  Type:PROTEIN  Length:85
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:85
                                    13        23        33        43        53        63        73        83     
          Q4KGC5_PSEF5    4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERDL 88
               SCOP domains d2obkb_ B: automated matches                                                          SCOP domains
               CATH domains 2obkB00 B:4-88 Glutaredoxin                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhhhh.....eeeeeee....eeeee..eeeee........hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  2obk B  4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERDL 88
                                    13        23        33        43        53        63        73        83

Chain C from PDB  Type:PROTEIN  Length:82
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:82
                                    12        22        32        42        52        62        72        82  
          Q4KGC5_PSEF5    3 ERKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDP 84
               SCOP domains d2obkc_ C: automated matches                                                       SCOP domains
               CATH domains 2obkC00 C:3-84 Glutaredoxin                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....hhhhhhhhhhhhhh.......eeeeeee....eeeee..eeeeehhhhh...hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  2obk C  3 ERKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDP 84
                                    12        22        32        42        52        62        72        82

Chain D from PDB  Type:PROTEIN  Length:84
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:84
                                    13        23        33        43        53        63        73        83    
          Q4KGC5_PSEF5    4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
               SCOP domains d2obkd_ D: automated matches                                                         SCOP domains
               CATH domains 2obkD00 D:4-87 Glutaredoxin                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhhhh.....eeeeeee....eeeee..eeeeehhhhh...hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2obk D  4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
                                    13        23        33        43        53        63        73        83

Chain E from PDB  Type:PROTEIN  Length:80
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:80
                                    14        24        34        44        54        64        74        84
          Q4KGC5_PSEF5    5 KPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDP 84
               SCOP domains d2obke_ E: automated matches                                                     SCOP domains
               CATH domains 2obkE00 E:5-84 Glutaredoxin                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhh.....eeeeeee....eeeee..eeeeehhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  2obk E  5 KPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDP 84
                                    14        24        34        44        54        64        74        84

Chain F from PDB  Type:PROTEIN  Length:86
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:86
                                    13        23        33        43        53        63        73        83      
          Q4KGC5_PSEF5    4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERDLG 89
               SCOP domains d2obkf_ F: automated matches                                                           SCOP domains
               CATH domains 2obkF00 F:4-89 Glutaredoxin                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhhhh.....eeeeeee....eeeee..eeeeehhhhh...hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  2obk F  4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERDLG 89
                                    13        23        33        43        53        63        73        83

Chain G from PDB  Type:PROTEIN  Length:84
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:84
                                    13        23        33        43        53        63        73        83    
          Q4KGC5_PSEF5    4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
               SCOP domains d2obkg_ G: automated matches                                                         SCOP domains
               CATH domains 2obkG00 G:4-87 Glutaredoxin                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhhhh........eeeeee.....eeee...eeee........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2obk G  4 RKPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
                                    13        23        33        43        53        63        73        83

Chain H from PDB  Type:PROTEIN  Length:83
 aligned with Q4KGC5_PSEF5 | Q4KGC5 from UniProtKB/TrEMBL  Length:95

    Alignment length:83
                                    14        24        34        44        54        64        74        84   
          Q4KGC5_PSEF5    5 KPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
               SCOP domains d2obkh_ H: automated matches                                                        SCOP domains
               CATH domains 2obkH00 H:5-87 Glutaredoxin                                                         CATH domains
           Pfam domains (1) -Rdx-2obkH01 H:6-81                                                          ------ Pfam domains (1)
           Pfam domains (2) -Rdx-2obkH02 H:6-81                                                          ------ Pfam domains (2)
           Pfam domains (3) -Rdx-2obkH03 H:6-81                                                          ------ Pfam domains (3)
           Pfam domains (4) -Rdx-2obkH04 H:6-81                                                          ------ Pfam domains (4)
           Pfam domains (5) -Rdx-2obkH05 H:6-81                                                          ------ Pfam domains (5)
           Pfam domains (6) -Rdx-2obkH06 H:6-81                                                          ------ Pfam domains (6)
           Pfam domains (7) -Rdx-2obkH07 H:6-81                                                          ------ Pfam domains (7)
           Pfam domains (8) -Rdx-2obkH08 H:6-81                                                          ------ Pfam domains (8)
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhh.....eeeeeee....eeeee..eeeeehhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  2obk H  5 KPEVIITYCTQCQWLLRAAWLAQELLSTFSDDLGKVSLEPATGGAFRITCDGVQIWERKADGGFPEAKVLKQRVRDQIDPERD 87
                                    14        24        34        44        54        64        74        84

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: Selenoprotein W-related (7)

Protein domain: automated matches (4)

Pseudomonas fluorescens [TaxId: 220664] (1)

1a	d2obka_	A:
1b	d2obkb_	B:
1c	d2obkc_	C:
1d	d2obkd_	D:
1e	d2obke_	E:
1f	d2obkf_	F:
1g	d2obkg_	G:
1h	d2obkh_	H:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Pseudomonas fluorescens pf-5. Organism_taxid: 220664. Strain: pf-5. (1)

1a	2obkF00	F:4-89
1b	2obkB00	B:4-88
1c	2obkA00	A:4-87
1d	2obkD00	D:4-87
1e	2obkG00	G:4-87
1f	2obkH00	H:5-87
1g	2obkC00	C:3-84
1h	2obkE00	E:5-84

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Rdx] (5)

Family: Rdx (5)

Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477) (1)

1a	Rdx-2obkH01	H:6-81
1b	Rdx-2obkH02	H:6-81
1c	Rdx-2obkH03	H:6-81
1d	Rdx-2obkH04	H:6-81
1e	Rdx-2obkH05	H:6-81
1f	Rdx-2obkH06	H:6-81
1g	Rdx-2obkH07	H:6-81
1h	Rdx-2obkH08	H:6-81

Asymmetric Unit(hide GO term definitions)

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

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
(no "Ligands, Modified Residues, Ions" information available for 2obk)

	Sites
(no "Sites" information available for 2obk)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2obk)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 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
	2obk
		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
	Q4KGC5_PSEF5 \| Q4KGC5
		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
	Q4KGC5_PSEF5 \| Q4KGC5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2OBK)

2fa8	PROTEIN WITH 69% OF THE HOMOLOGY
plr6

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 8)

CATH Domains (1, 8)

Pfam Domains (1, 8)

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