3OX3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   X-RAY STRUCTURAL STUDY OF QUINONE REDUCTASE II INHIBITION BY COMPOUNDS WITH MICROMOLAR TO NANOMOLAR RANGE IC50 VALUES

Authors :   S. D. Pegan, M. Sturdy, G. Ferry, P. Delagrange, J. A. Boutin, A. D. Mesec

Date :   21 Sep 10 (Deposition) - 25 May 11 (Release) - 06 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Qr2, Nq02, Flavoprotein, Metal-2 Binding, Oxidoreductase, Phosphoprotein, Fad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Pegan, M. Sturdy, G. Ferry, P. Delagrange, J. A. Boutin, A. D. Mesecar
X-Ray Structural Studies Of Quinone Reductase 2 Nanomolar Range Inhibitors.
Protein Sci. V. 20 1182 2011
PubMed-ID: 21538647 | Reference-DOI: 10.1002/PRO.647

Molecule 1 - RIBOSYLDIHYDRONICOTINAMIDE DEHYDROGENASE [QUINONE]
	Chains	:	A, B
	EC Number	:	1.10.99.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NQO2, NMOR2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	4X4	2	Ligand/Ion	N-[2-(2-METHOXY-1H-DIPYRIDO[2,3-A:3',2'-E]PYRROLIZIN-11-YL)ETHYL]FURAN-2-CARBOXAMIDE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:173 , HIS A:177 , CYS A:222	BINDING SITE FOR RESIDUE ZN A 231
2	AC2	SOFTWARE	HIS A:11 , LYS A:15 , SER A:16 , PHE A:17 , ASN A:18 , SER A:20 , PRO A:102 , LEU A:103 , TYR A:104 , TRP A:105 , PHE A:106 , THR A:147 , THR A:148 , GLY A:149 , GLY A:150 , TYR A:155 , GLU A:193 , GLU A:197 , ARG A:200 , HOH A:267 , HOH A:293 , HOH A:353 , ASN B:66 , GLY B:68 , ASP B:117 , 4X4 B:233	BINDING SITE FOR RESIDUE FAD A 232
3	AC3	SOFTWARE	GLY A:68 , GLN A:122 , PHE A:126 , GLY A:174 , PHE A:178 , TRP B:105 , PHE B:106 , MET B:154 , ILE B:194 , FAD B:232 , HOH B:426	BINDING SITE FOR RESIDUE 4X4 A 233
4	AC4	SOFTWARE	HIS B:173 , HIS B:177 , CYS B:222	BINDING SITE FOR RESIDUE ZN B 231
5	AC5	SOFTWARE	ASN A:66 , ASP A:117 , 4X4 A:233 , HIS B:11 , LYS B:15 , SER B:16 , PHE B:17 , ASN B:18 , SER B:20 , PRO B:102 , LEU B:103 , TYR B:104 , TRP B:105 , PHE B:106 , THR B:147 , THR B:148 , GLY B:149 , GLY B:150 , TYR B:155 , GLU B:193 , ARG B:200 , HOH B:293 , HOH B:441 , HOH B:445	BINDING SITE FOR RESIDUE FAD B 232
6	AC6	SOFTWARE	TRP A:105 , PHE A:106 , GLY A:149 , MET A:154 , FAD A:232 , HOH A:363 , GLY B:68 , PHE B:126 , GLY B:174 , PHE B:178 , HOH B:425	BINDING SITE FOR RESIDUE 4X4 B 233

(no "SS Bond" information available for 3OX3)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:128	-	Pro A:129
2	Ala A:195	-	Ser A:196
3	Ile B:128	-	Pro B:129

Asymmetric/Biological Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_021399	K	16	R	NQO2_HUMAN	Polymorphism	28383623	A/B	K	15	R
2	UniProt	VAR_021400	E	29	G	NQO2_HUMAN	Polymorphism	17136117	A/B	E	28	G
3	UniProt	VAR_021401	L	47	F	NQO2_HUMAN	Polymorphism	1143684	A/B	F	46	F
4	UniProt	VAR_021402	G	58	D	NQO2_HUMAN	Polymorphism	17300141	A/B	G	57	D
5	UniProt	VAR_021403	V	184	A	NQO2_HUMAN	Polymorphism	28383651	A/B	V	183	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3OX3)

Asymmetric/Biological Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.5d	ENST00000380455	5d	ENSE00001728408	chr6:3000231-3000319	89	NQO2_HUMAN	-	0	0	-	-
1.10	ENST00000380455	10	ENSE00001777236	chr6:3006702-3006793	92	NQO2_HUMAN	1-3	3	2	A:2-2 B:2-2	1 1
1.11	ENST00000380455	11	ENSE00001083962	chr6:3010259-3010423	165	NQO2_HUMAN	3-58	56	2	A:2-57 B:2-57	56 56
1.12b	ENST00000380455	12b	ENSE00000847812	chr6:3012778-3012908	131	NQO2_HUMAN	58-101	44	2	A:57-100 B:57-100	44 44
1.13	ENST00000380455	13	ENSE00002196995	chr6:3015764-3015877	114	NQO2_HUMAN	102-139	38	2	A:101-138 B:101-138	38 38
1.14	ENST00000380455	14	ENSE00000680401	chr6:3017118-3017219	102	NQO2_HUMAN	140-173	34	2	A:139-172 B:139-172	34 34
1.15b	ENST00000380455	15b	ENSE00001358191	chr6:3019713-3019996	284	NQO2_HUMAN	174-231	58	2	A:173-228 B:173-229	56 57

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:227
 aligned with NQO2_HUMAN | P16083 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       
           NQO2_HUMAN     3 GKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNLEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHF 229
               SCOP domains d3ox3a_ A: Quinone reductase type 2 (menadione reductase)                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhh..eeeeee..........hhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh..........hhhhh.....eeeeeee...hhhhhh......hhhhhhhhhhh........ee...eee.hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------R------------G-----------------F----------D-----------------------------------------------------------------------------------------------------------------------------A--------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1------------------------------------------------------Exon 1.12b  PDB: A:57-100 UniProt: 58-101   Exon 1.13  PDB: A:101-138             Exon 1.14  PDB: A:139-172         Exon 1.15b  PDB: A:173-228 UniProt: 174-231 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) Exon 1.11  PDB: A:2-57 UniProt: 3-58                    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3ox3 A   2 GKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNFEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHF 228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with NQO2_HUMAN | P16083 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
           NQO2_HUMAN     3 GKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNLEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHFG 230
               SCOP domains d3ox3b_ B: Quinone reductase type 2 (menadione reductase)                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -Flavodoxin_2-3ox3B01 B:3-211                                                                                                                                                                                     ------------------ Pfam domains (1)
           Pfam domains (2) -Flavodoxin_2-3ox3B02 B:3-211                                                                                                                                                                                     ------------------ Pfam domains (2)
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhhh.eeeeee..........hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh..........hhhhh.....eeeeeee...............hhhhhhhhhhh........ee...eee......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------R------------G-----------------F----------D-----------------------------------------------------------------------------------------------------------------------------A---------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1------------------------------------------------------Exon 1.12b  PDB: B:57-100 UniProt: 58-101   Exon 1.13  PDB: B:101-138             Exon 1.14  PDB: B:139-172         Exon 1.15b  PDB: B:173-229 UniProt: 174-231 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) Exon 1.11  PDB: B:2-57 UniProt: 3-58                    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3ox3 B   2 GKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNFEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHFG 229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

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

Fold: Flavodoxin-like (1057)

Superfamily: Flavoproteins (208)

Family: Quinone reductase (65)

Protein domain: Quinone reductase type 2 (menadione reductase) (44)

Human (Homo sapiens) [TaxId: 9606] (44)

1a	d3ox3a_	A:
1b	d3ox3b_	B:

(no "CATH Domain" information available for 3OX3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Flavoprotein (71)

Family: Flavodoxin_2 (35)

Homo sapiens (Human) (22)

1a	Flavodoxin_2-3ox3B01	B:3-211
1b	Flavodoxin_2-3ox3B02	B:3-211

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NQO2_HUMAN | P16083)

molecular function
	GO:0008753	NADPH dehydrogenase (quinone) activity	Catalysis of the reaction: NADPH + H+ + a quinone = NADP+ + a quinol.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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).
biological process
	GO:0007613	memory	The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:195 - Ser A:196	[ RasMol ]
		Ile A:128 - Pro A:129	[ RasMol ]
		Ile B:128 - Pro B:129	[ RasMol ]

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	3ox3
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	NQO2_HUMAN \| P16083
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	1.10.99.2
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 10)

PROSITE Motifs (0, 0)

Exons (6, 12)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

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