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(-) Description

Title :  CRYSTAL STRUCTURE OF QUINONE REDUCTASE II IN COMPLEX WITH A 2-(4-METHOXY-PHENYL)-5-METHOXY-INDOL-3-ONE MOLECULE
 
Authors :  S. Sirigu, F. Nepveu, L. Vuillard, G. Ferry, T. Isabet, A. Thompson, J. A
Date :  19 Dec 14  (Deposition) - 13 Jan 16  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Qr2, Fad, Flavoprotein, Metal-Binding, Oxidoreductase, Indolone Oxide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. E. Cassagnes, N. Rakotoarivelo, S. Sirigu, P. Perio, E. Najahi, L. M. Chavas, A. Thompson, R. Gayon, G. Ferry, J. A. Boutin, A. Valentin K. Reybier, F. Nepveu
Role Of Quinone Reductase 2 In The Antimalarial Properties Of Indolone-Type Derivatives.
Molecules V. 22 2017
PubMed-ID: 28146103  |  Reference-DOI: 10.3390/MOLECULES22020210

(-) Compounds

Molecule 1 - RIBOSYLDIHYDRONICOTINAMIDE DEHYDROGENASE [QUINONE]
    Chains: A, B
    EC Number: 1.10.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NQO2, NMOR2
    Nrh: QUINONE OXIDOREDUCTASE 2,QUINONE REDUCTASE 2,QR2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: QUINONE REDUCTASE II,NRH DEHYDROGENASE [QUINONE] 2,

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
13ZV2Ligand/Ion5-METHOXY-2-(4-METHOXYPHENYL)-3H-INDOL-3-ONE
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO43Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:173 , HIS A:177 , CYS A:222binding site for residue ZN A 301
2AC2SOFTWAREHIS 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 , ARG A:200 , 3ZV A:303 , HOH A:470 , HOH A:495 , HOH A:505 , HOH A:509 , ASN B:66 , ASP B:117 , HOH B:473binding site for residue FAD A 302
3AC3SOFTWARETRP A:105 , GLY A:149 , MET A:154 , ILE A:194 , FAD A:302 , HOH A:475 , HOH A:494 , PHE B:126binding site for residue 3ZV A 303
4AC4SOFTWAREARG A:78 , GLU A:197 , GLU A:198 , ARG A:200binding site for residue SO4 A 304
5AC5SOFTWAREGLU A:47 , ARG A:49 , HOH A:506 , GLU B:47 , ARG B:49binding site for residue SO4 A 305
6AC6SOFTWAREGLU A:47 , LYS A:53 , ASP A:54 , ALA A:81 , ASP A:83 , ARG A:118 , HOH A:501binding site for residue SO4 A 306
7AC7SOFTWAREHIS B:173 , HIS B:177 , CYS B:222binding site for residue ZN B 301
8AC8SOFTWAREASN A:66 , ASP A:117 , 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 , 3ZV B:303 , HOH B:511 , HOH B:518 , HOH B:521 , HOH B:522 , HOH B:540binding site for residue FAD B 302
9AC9SOFTWAREPHE A:126 , ILE A:128 , PHE A:178 , TRP B:105 , GLY B:149 , MET B:154 , ILE B:194 , FAD B:302 , HOH B:519binding site for residue 3ZV B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XDH)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ile A:128 -Pro A:129
2Pro A:129 -Gly A:130
3Ile B:128 -Pro B:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XDH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XDH)

(-) Exons   (0, 0)

(no "Exon" information available for 4XDH)

(-) Sequences/Alignments

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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhhh.eeeeee..........hhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh..........hhhhh.....eeeeeee...............hhhhhhhhhhh........ee...eee......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdh A   2 GKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNFEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHFGQ 230
                                    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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhh..eeeeee..........hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh..........hhhhh.....eeeeeee...............hhhhhhhhhhh........ee...eee......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdh B   1 AGKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNFEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHFGQ 230
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4XDH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XDH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XDH)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ile A:128 - Pro A:129   [ RasMol ]  
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    Pro A:129 - Gly A:130   [ RasMol ]  
 

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  4xdh
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NQO2_HUMAN | P16083: 1qr2 1sg0 1xi2 1zx1 2bzs 2qmy 2qmz 2qr2 2qwx 2qx4 2qx6 2qx8 2qx9 3fw1 3g5m 3gam 3nfr 3nhf 3nhj 3nhk 3nhl 3nhp 3nhr 3nhs 3nhu 3nhw 3nhy 3o2n 3o73 3ovm 3owh 3owx 3ox1 3ox2 3ox3 3te7 3tem 3tzb 3uxe 3uxh 4fgj 4fgk 4fgl 4gqi 4gr9 4qod 4qoe 4qof 4qog 4qoh 4qoi 4qoj 4u7f 4u7g 4u7h 4xdg 4zvk 4zvl 4zvm 4zvn 5buc 5lbt 5lbu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4XDH)