3W78 - 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)

Title :   CRYSTAL STRUCTURE OF AZOREDUCTASE AZRC IN COMPLEX WITH NAD(P)-INHIBITOR CIBACRON BLUE

Authors :   J. Yu, D. Ogata, T. Ooi, M. Yao

Date :   27 Feb 13 (Deposition) - 12 Feb 14 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.62

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

Keywords :   Azoreductase, Azo Bond Cleavage, Fmn-Binding, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Yu, D. Ogata, Z. Gai, S. Taguchi, I. Tanaka, T. Ooi, M. Yao
Structures Of Azra And Of Azrc Complexed With Substrate Or Inhibitor: Insight Into Substrate Specificity And Catalytic Mechanism
Acta Crystallogr. , Sect. D V. 70 553 2014
PubMed: search | Reference-DOI: 10.1107/S1399004713030988

Molecule 1 - FMN-DEPENDENT NADH-AZOREDUCTASE
	Chains	:	A, D, B, C
	EC Number	:	1.7.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AZRC, AZOR
	Organism Scientific	:	BACILLUS
	Organism Taxid	:	391699
	Strain	:	B29
	Synonym	:	AZO-DYE REDUCTASE, FMN-DEPENDENT NADH-AZO COMPOUND OXIDOREDUCTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CBD	4	Ligand/Ion	CIBACRON BLUE
2	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CBD	2	Ligand/Ion	CIBACRON BLUE
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CBD	2	Ligand/Ion	CIBACRON BLUE
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	CBD	2	Ligand/Ion	CIBACRON BLUE
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:10 , SER A:17 , PHE A:18 , GLY A:19 , PRO A:101 , MET A:102 , TRP A:103 , ASN A:104 , PHE A:105 , ALA A:146 , GLY A:148 , GLY A:149 , TYR A:151 , ASN A:187 , PHE B:57 , CBD B:302	BINDING SITE FOR RESIDUE FMN A 301
2	AC2	SOFTWARE	ALA A:119 , PHE A:125 , TYR A:127 , THR A:128 , GLU A:129 , ASN A:130 , GLY A:131 , PRO A:132 , PHE A:172 , HOH A:401 , ASN B:104 , GLY B:149 , VAL B:150 , TYR B:151 , TYR B:156 , ASN B:187 , ALA B:188 , FMN B:301	BINDING SITE FOR RESIDUE CBD A 302
3	AC3	SOFTWARE	ASN D:10 , SER D:17 , PHE D:18 , GLY D:19 , PHE D:57 , PRO D:101 , MET D:102 , TRP D:103 , ASN D:104 , PHE D:105 , ALA D:146 , THR D:147 , GLY D:148 , GLY D:149 , TYR D:151 , ASN D:187 , CBD D:302	BINDING SITE FOR RESIDUE FMN D 301
4	AC4	SOFTWARE	ASN D:104 , ALA D:119 , PHE D:125 , TYR D:127 , THR D:128 , ASN D:130 , PRO D:132 , GLY D:149 , VAL D:150 , TYR D:151 , PHE D:172 , ASN D:187 , ALA D:188 , FMN D:301 , HOH D:401	BINDING SITE FOR RESIDUE CBD D 302
5	AC5	SOFTWARE	CBD A:302 , ASN B:10 , SER B:17 , PHE B:18 , GLY B:19 , PRO B:101 , MET B:102 , TRP B:103 , ASN B:104 , PHE B:105 , ALA B:146 , THR B:147 , GLY B:148 , GLY B:149 , TYR B:151 , MET B:186 , ASN B:187	BINDING SITE FOR RESIDUE FMN B 301
6	AC6	SOFTWARE	ASN A:104 , VAL A:150 , TYR A:151 , ASN A:187 , ALA A:188 , FMN A:301 , ALA B:119 , PHE B:125 , TYR B:127 , GLU B:129 , ASN B:130 , GLY B:131 , PRO B:132 , PHE B:172	BINDING SITE FOR RESIDUE CBD B 302
7	AC7	SOFTWARE	ASN C:10 , SER C:17 , PHE C:18 , GLY C:19 , PHE C:57 , PRO C:101 , MET C:102 , TRP C:103 , ASN C:104 , PHE C:105 , ALA C:146 , GLY C:148 , GLY C:149 , TYR C:151 , CBD C:302	BINDING SITE FOR RESIDUE FMN C 301
8	AC8	SOFTWARE	ASN C:104 , ALA C:119 , PHE C:125 , TYR C:127 , THR C:128 , GLU C:129 , ASN C:130 , PRO C:132 , GLY C:149 , VAL C:150 , TYR C:151 , TYR C:156 , ASN C:187 , ALA C:188 , FMN C:301	BINDING SITE FOR RESIDUE CBD C 302

(no "SS Bond" information available for 3W78)

Asymmetric Unit

No.	Residues
1	Glu D:191	-	Lys D:192
2	Val C:40	-	Thr C:41
3	Gly C:185	-	Met C:186
4	Ala C:188	-	Asn C:189

(no "SAP(SNP)/Variant" information available for 3W78)

(no "PROSITE Motif" information available for 3W78)

(no "Exon" information available for 3W78)

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:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....ee......ee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w78 A   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhhhh...eeeeee.hhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....eeee..eeee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w78 B   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain C from PDB  Type:PROTEIN  Length:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhhhhhhh.......ee.hhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhh.....ee......ee.....eeeeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w78 C   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain D from PDB  Type:PROTEIN  Length:210
 aligned with C0STY1_9BACI | C0STY1 from UniProtKB/TrEMBL  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
         C0STY1_9BACI     2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........hhhhhhhhhhhhhhhh.....eeeeee.hhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh.....ee......ee.....eeeeeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeeeee.......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w78 D   2 TKVLFITANPNSAEGSFGMAVGEAFIEAYKNEHPQDEVVTIDLFNTTVPAIDADVFAAWGKFAAGEGFEALTEVQQQKVAAMNTNLETFMNADRYVFVTPMWNFSYPPVVKAYLDNVAIAGKTFKYTENGPVGLLEGKKALHIQATGGVYSEGAYAAVDFGRNHLKTVLGFVGVNDTEYIAVEGMNANPEKAQEIKEAAIANARELAKRF 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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 '\|'

(no "SCOP Domain" information available for 3W78)

(no "CATH Domain" information available for 3W78)

(no "Pfam Domain" information available for 3W78)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (C0STY1_9BACI | C0STY1)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0008752	FMN reductase activity	Catalysis of the reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016652	oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0016661	oxidoreductase activity, acting on other nitrogenous compounds as donors	Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
	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.

Asymmetric Unit
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		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala C:188 - Asn C:189	[ RasMol ]
		Glu D:191 - Lys D:192	[ RasMol ]
		Gly C:185 - Met C:186	[ RasMol ]
		Val C:40 - Thr C:41	[ RasMol ]

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	3w78
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	1.7.-.-
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	C0STY1_9BACI \| C0STY1	:	3w79 3w7a

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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