2BJ3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   NIKR-APO

Authors :   T. H. Tahirov

Date :   28 Jan 05 (Deposition) - 08 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Transcription, Repressor, Pyrococcus Horikoshii, Nikr, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. T. Chivers, T. H. Tahirov
Structure Of Pyrococcus Horikoshii Nikr: Nickel Sensing And Implications For The Regulation Of Dna Recognition
J. Mol. Biol. V. 348 597 2005
PubMed-ID: 15826657 | Reference-DOI: 10.1016/J.JMB.2005.03.017
(for further references see the PDB file header)

Molecule 1 - NICKEL RESPONSIVE REGULATOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:47 , THR B:131 , SER B:132 , THR B:133 , GLY B:134 , LYS B:135 , GLU B:136	BINDING SITE FOR RESIDUE CL B1140
2	AC2	SOFTWARE	TRP C:47 , SER C:132 , THR C:133 , LYS C:135 , GLU C:136	BINDING SITE FOR RESIDUE CL C1139
3	AC3	SOFTWARE	HOH A:2026 , HOH A:2027 , HOH A:2028 , ILE B:25 , HOH B:2004 , HOH B:2005 , HOH B:2006	BINDING SITE FOR RESIDUE MG B1139
4	AC4	SOFTWARE	HOH C:2001 , HOH C:2002 , HOH D:2014 , HOH D:2023 , HOH D:2024 , HOH D:2025	BINDING SITE FOR RESIDUE MG D1134

(no "SS Bond" information available for 2BJ3)

(no "Cis Peptide Bond" information available for 2BJ3)

(no "SAP(SNP)/Variant" information available for 2BJ3)

(no "PROSITE Motif" information available for 2BJ3)

(no "Exon" information available for 2BJ3)

Asymmetric/Biological 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:136
 aligned with NIKR_PYRHO | O58316 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      
           NIKR_PYRHO     1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKE 136
               SCOP domains d2bj3a1 A:1-50                                    d2bj3a2 A:51-136 Nickel responsive regulator NikR, C-terminal domain                   SCOP domains
               CATH domains --------2bj3A01 A:9-50 Met repressor-like         -------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhh..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bj3 A   1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKE 136
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with NIKR_PYRHO | O58316 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
           NIKR_PYRHO     2 ELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKELV 138
               SCOP domains d2bj3b1 B:2-50                                   d2bj3b2 B:51-138 Nickel responsive regulator NikR, C-terminal domain                     SCOP domains
               CATH domains ---------2bj3B01 B:11-50 Met repressor-like      ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bj3 B   2 ELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKELV 138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with NIKR_PYRHO | O58316 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
           NIKR_PYRHO     1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKELV 138
               SCOP domains d2bj3c1 C:1-50                                    d2bj3c2 C:51-138 Nickel responsive regulator NikR, C-terminal domain                     SCOP domains
               CATH domains ----------2bj3C01 C:11-50 Met repressor-like      ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeeeeeeehhhhhhhhhhhhhh..eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bj3 C   1 MELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTGKELV 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:131
 aligned with NIKR_PYRHO | O58316 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
           NIKR_PYRHO     2 ELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNHDEGDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTG 134
               SCOP domains d2bj3d1 D:2-50                                   d2bj3d2 D:51-1  34 Nickel responsive regulator NikR, C-terminal domain               SCOP domains
               CATH domains ---------2bj3D01 D:11-50 Met repressor-like      ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee..--hhhhhhhhhhhhhh...eeeeeee......eeeeeeeeeehhhhhhhhhhhhh...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bj3 D   2 ELIRFSISIPSKLLEKFDQIIEEIGYENRSEAIRDLIRDFIIRHEWEVGNEEVAGTITIVYNH--GDVVKALLDLQHEYLDEIISSLHVHMDEHNCLEVIVVKGEAKKIKMIADKLLSLKGVKHGKLVMTSTG 134
                                    11        21        31        41        51        61  |  |  71        81        91       101       111       121       131   
                                                                                         64 67

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ribbon-helix-helix (65)

Superfamily: Ribbon-helix-helix (65)

Family: CopG-like (13)

Protein domain: Nickel responsive regulator NikR, N-terminal domain (8)

Pyrococcus horikoshii [TaxId: 53953] (4)

1a	d2bj3a1	A:1-50
1b	d2bj3b1	B:2-50
1c	d2bj3c1	C:1-50
1d	d2bj3d1	D:2-50

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: ACT-like (63)

Family: Nickel responsive regulator NikR, C-terminal domain (14)

Protein domain: Nickel responsive regulator NikR, C-terminal domain (12)

Pyrococcus horikoshii [TaxId: 53953] (4)

2a	d2bj3a2	A:51-136
2b	d2bj3b2	B:51-138
2c	d2bj3c2	C:51-138
2d	d2bj3d2	D:51-134

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant (30)

Homologous Superfamily: Met repressor-like (30)

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. (5)

1a	2bj3A01	A:9-50
1b	2bj3B01	B:11-50
1c	2bj3C01	C:11-50
1d	2bj3D01	D:11-50

(no "Pfam Domain" information available for 2BJ3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (NIKR_PYRHO | O58316)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0010045	response to nickel cation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nickel cation stimulus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric/Biological 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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bj3)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	2bj3
		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
	NIKR_PYRHO \| O58316
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	NIKR_PYRHO \| O58316
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NIKR_PYRHO \| O58316	:	2bj1 2bj7 2bj8 2bj9

2bj1	NIKR IN OPEN CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
2bj7	NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
2bj9	NIKR WITH BOUND NICKEL AND PHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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 (2, 8)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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