2BT6 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   RU(BPY)2(MBPY)-MODIFIED BOVINE ADRENODOXIN

Authors :   A. Halavaty, J. J. Mueller, J. Contzen, C. Jung, F. Hannemann, R. Bernha M. Galander, F. Lendzian, U. Heinemann

Date :   26 May 05 (Deposition) - 25 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Ruthenium(Ii) Bipyridyl Complex, Intramolecular Electron Transfer, Electron Transport, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Halavaty, J. J. Mueller, J. Contzen, C. Jung, F. Hannemann, R. Bernhardt, M. Galander, F. Lendzian, U. Heinemann
Light-Induced Reduction Of Bovine Adrenodoxin Via The Covalently Bound Ruthenium(Ii) Bipyridyl Complex: Intramolecular Electron Transfer And Crystal Structure.
Biochemistry V. 45 709 2006
PubMed-ID: 16411746 | Reference-DOI: 10.1021/BI0510330

Molecule 1 - ADRENODOXIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET3D
	Fragment	:	RESIDUES 63-166
	Organ	:	ADRENAL CORTEX
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	COVALENT LINK BETWEEN CYS95 AND C39 ATOM OF RU(BPY)2(MBPY) PER EACH CHAIN IN ASYMMETRIC UNIT
	Synonym	:	BOVINE ADRENODOXIN, ADRENAL FERREDOXIN

		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 (3, 5)

No.	Name	Count	Type	Full Name
1	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	RUA	2	Ligand/Ion	(4'-METHYL-2,2'BIPYRIDINE)BIS(2,2'-BIPYRIDINE)

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	RUA	1	Ligand/Ion	(4'-METHYL-2,2'BIPYRIDINE)BIS(2,2'-BIPYRIDINE)

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	RUA	1	Ligand/Ion	(4'-METHYL-2,2'BIPYRIDINE)BIS(2,2'-BIPYRIDINE)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2055 , HOH A:2056 , HOH A:2118 , HOH B:2019	BINDING SITE FOR RESIDUE MG B1111
2	AC2	SOFTWARE	GLY A:44 , CYS A:46 , GLY A:48 , LEU A:50 , CYS A:52 , CYS A:55 , CYS A:92	BINDING SITE FOR RESIDUE FES A1109
3	AC3	SOFTWARE	SER A:28 , GLY A:48 , CYS A:92 , GLN A:93 , CYS A:95 , HOH A:2024 , THR B:71 , GLU B:73 , GLN B:93 , RUA B:1110	BINDING SITE FOR RESIDUE RUA A1110
4	AC4	SOFTWARE	GLY B:44 , CYS B:46 , GLY B:48 , LEU B:50 , CYS B:52 , CYS B:55 , CYS B:92	BINDING SITE FOR RESIDUE FES B1109
5	AC5	SOFTWARE	ALA A:69 , THR A:71 , GLU A:73 , GLN A:93 , RUA A:1110 , GLY B:48 , CYS B:92 , GLN B:93 , CYS B:95	BINDING SITE FOR CHAIN B OF RESIDUES 1110 TO 1110

(no "SS Bond" information available for 2BT6)

(no "Cis Peptide Bond" information available for 2BT6)

(no "SAP(SNP)/Variant" information available for 2BT6)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	ADX_BOVIN	65-169	2	A:7-108 B:7-108
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	ADX_BOVIN	104-114	2	A:46-56 B:46-56

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	ADX_BOVIN	65-169	1	A:7-108 -
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	ADX_BOVIN	104-114	1	A:46-56 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	ADX_BOVIN	65-169	1	- B:7-108
2	ADX	PS00814	Adrenodoxin family, iron-sulfur binding region signature.	ADX_BOVIN	104-114	1	- B:46-56

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENSBTAT00000015660	2	ENSBTAE00000127216	chr15:18520776-18521119	344	ADX_BOVIN	1-64	64	2	A:4-6 (gaps) B:5-6	10 2
1.3	ENSBTAT00000015660	3	ENSBTAE00000127236	chr15:18526683-18526807	125	ADX_BOVIN	64-106	43	2	A:6-48 B:6-48	43 43
1.4	ENSBTAT00000015660	4	ENSBTAE00000127241	chr15:18545168-18545297	130	ADX_BOVIN	106-149	44	2	A:48-91 B:48-91	44 44
1.5	ENSBTAT00000015660	5	ENSBTAE00000359886	chr15:18555251-18556187	937	ADX_BOVIN	149-190	42	2	A:91-108 B:91-108	18 18

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:105
 aligned with ADX_BOVIN | P00257 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:112
                                    64        74        84        94       104       114       124       134       144       154       164  
            ADX_BOVIN    55 GRAQSSSEDKITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDLAYGLTDRSRLGCQICLTKAMDNMTVRVP 166
               SCOP domains d       2bt6a_ A: automated matches                                                                              SCOP domains
               CATH domains 2       bt6A00 A:4-108  [code=3.10.20.30, no name defined]                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-------.eeeeeee.....eeeeeee...hhhhhhhhh...................eee.hhhhhh.....hhhhhhhhh........eee.hhh..hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------2FE2S_FER_2  PDB: A:7-108 UniProt: 65-169                                                              PROSITE (1)
                PROSITE (2) -------------------------------------------------ADX        ---------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  -----------------------------------------Exon 1.4  PDB: A:48-91 UniProt: 106-149     ----------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.3  PDB: A:6-48 UniProt: 64-106      ------------------------------------------Exon 1.5           Transcript 1 (2)
                 2bt6 A   4 G-------DKITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDLAYGLTDRSRLGCQICLTKAMDNMTVRVP 108
                            |       |6        16        26        36        46        56        66        76        86        96       106  
                            |       5                                                                                                       
                            4

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with ADX_BOVIN | P00257 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:104
                                    72        82        92       102       112       122       132       142       152       162    
            ADX_BOVIN    63 DKITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDLAYGLTDRSRLGCQICLTKAMDNMTVRVP 166
               SCOP domains d2bt6b_ B: automated matches                                                                             SCOP domains
               CATH domains 2bt6B00 B:5-108  [code=3.10.20.30, no name defined]                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeee...hhhhhhhhh...................eee.hhhhhh.....hhhhhhhhh........eee.hhh..hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: B:7-108 UniProt: 65-169                                                              PROSITE (1)
                PROSITE (2) -----------------------------------------ADX        ---------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.-----------------------------------------Exon 1.4  PDB: B:48-91 UniProt: 106-149     ----------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: B:6-48 UniProt: 64-106      ------------------------------------------Exon 1.5           Transcript 1 (2)
                 2bt6 B   5 DKITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDLAYGLTDRSRLGCQICLTKAMDNMTVRVP 108
                                    14        24        34        44        54        64        74        84        94       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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: 2Fe-2S ferredoxin-like (174)

Family: 2Fe-2S ferredoxin-related (74)

Protein domain: automated matches (14)

Cow (Bos taurus) [TaxId: 9913] (1)

1a	d2bt6a_	A:
1b	d2bt6b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.30, no name defined] (153)

Bovine (Bos taurus) (4)

1a	2bt6B00	B:5-108
1b	2bt6A00	A:4-108

(no "Pfam Domain" information available for 2BT6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ADX_BOVIN | P00257)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0042446	hormone biosynthetic process	The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006694	steroid biosynthetic process	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	2bt6
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UniProtKB/Swiss-Prot
	ADX_BOVIN \| P00257	:	1ayf 1cje 1e6e 1l6u 1l6v 2jqr

1ayf	BOVINE ADRENODOXIN (OXIDIZED)
1cje	ADRENODOXIN FROM BOVINE
1e6e	ADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 SYSTEMS
1l6u	NMR STRUCTURE OF OXIDIZED ADRENODOXIN
1l6v	STRUCTURE OF REDUCED BOVINE ADRENODOXIN

Description

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (4, 8)

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