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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC STRUCTURE ACTIVITY RELATIONSHIP (SAR) OF CASIMIROIN AND ITS ANALOGS BOUND TO HUMAN QUINONE REDUCTASE 2
 
Authors :  M. Sturdy
Date :  14 Jun 10  (Deposition) - 11 Jan 12  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Dimer, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sturdy
X-Ray Crystallographic Structure Activity Relationship (Sar Of Casimiroin And Its Analogs Bound To Human Quinone Reductase 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSYLDIHYDRONICOTINAMIDE DEHYDROGENASE [QUINONE]
    ChainsA, B
    EC Number1.10.99.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-23D
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNQO2, NMOR2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2YTR2Ligand/Ion7,8-DIMETHOXY-1,4-DIMETHYLQUINOLIN-2(1H)-ONE
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:173 , HIS A:177 , CYS A:222BINDING SITE FOR RESIDUE ZN A 231
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 , PRO A:192 , GLU A:193 , ARG A:200 , LYS A:201 , HOH A:354 , ASN B:66 , YTR B:233 , HOH B:308 , HOH B:413BINDING SITE FOR RESIDUE FAD A 232
3AC3SOFTWAREPHE A:126 , GLY A:174 , PHE A:178 , TRP B:105 , PHE B:106 , GLY B:150 , MET B:154 , ASN B:161 , FAD B:231BINDING SITE FOR RESIDUE YTR A 233
4AC4SOFTWAREHIS B:173 , HIS B:177 , CYS B:222BINDING SITE FOR RESIDUE ZN B 232
5AC5SOFTWAREASN A:66 , ASP A:117 , YTR A:233 , HOH A:344 , 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 , GLU B:197 , ARG B:200 , HOH B:370BINDING SITE FOR RESIDUE FAD B 231
6AC6SOFTWARETRP A:105 , PHE A:106 , GLY A:150 , ASN A:161 , FAD A:232 , PHE B:126 , GLY B:174 , PHE B:178BINDING SITE FOR RESIDUE YTR B 233

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric/Biological Unit (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021399K16RNQO2_HUMANPolymorphism28383623A/BK15R
2UniProtVAR_021400E29GNQO2_HUMANPolymorphism17136117A/BE28G
3UniProtVAR_021401L47FNQO2_HUMANPolymorphism1143684A/BF46F
4UniProtVAR_021402G58DNQO2_HUMANPolymorphism17300141A/BG57D
5UniProtVAR_021403V184ANQO2_HUMANPolymorphism28383651A/BV183A

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5dENST000003804555dENSE00001728408chr6:3000231-300031989NQO2_HUMAN-00--
1.10ENST0000038045510ENSE00001777236chr6:3006702-300679392NQO2_HUMAN1-332A:1-2
B:1-2
2
2
1.11ENST0000038045511ENSE00001083962chr6:3010259-3010423165NQO2_HUMAN3-58562A:2-57
B:2-57
56
56
1.12bENST0000038045512bENSE00000847812chr6:3012778-3012908131NQO2_HUMAN58-101442A:57-100
B:57-100
44
44
1.13ENST0000038045513ENSE00002196995chr6:3015764-3015877114NQO2_HUMAN102-139382A:101-138
B:101-138
38
38
1.14ENST0000038045514ENSE00000680401chr6:3017118-3017219102NQO2_HUMAN140-173342A:139-172
B:139-172
34
34
1.15bENST0000038045515bENSE00001358191chr6:3019713-3019996284NQO2_HUMAN174-231582A:173-230
B:173-230
58
58

(-) 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:230
 aligned with NQO2_HUMAN | P16083 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           NQO2_HUMAN     2 AGKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNLEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHFGQ 231
               SCOP domains d3nhla_ 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...............hhhhhhhhhhh..hhhhh.ee...eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh. 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:173-230 UniProt: 174-231                Transcript 1 (1)
           Transcript 1 (2) -Exon 1.11  PDB: A:2-57 UniProt: 3-58                    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3nhl A   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

Chain B from PDB  Type:PROTEIN  Length:230
 aligned with NQO2_HUMAN | P16083 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           NQO2_HUMAN     2 AGKKVLIVYAHQEPKSFNGSLKNVAVDELSRQGCTVTVSDLYAMNLEPRATDKDITGTLSNPEVFNYGVETHEAYKQRSLASDITDEQKKVREADLVIFQFPLYWFSVPAILKGWMDRVLCQGFAFDIPGFYDSGLLQGKLALLSVTTGGTAEMYTKTGVNGDSRYFLWPLQHGTLHFCGFKVLAPQISFAPEIASEEERKGMVAAWSQRLQTIWKEEPIPCTAHWHFGQ 231
               SCOP domains d3nhlb_ B: Quinone reductase type 2 (menadione reductase)                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhh..eeeeee..........hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh..........hhhhh.....eeeeeee...............hhhhhhhhhhh..hhhhh.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:173-230 UniProt: 174-231                Transcript 1 (1)
           Transcript 1 (2) -Exon 1.11  PDB: B:2-57 UniProt: 3-58                    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3nhl 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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NQO2_HUMAN | P160831qr2 1sg0 1xi2 1zx1 2bzs 2qmy 2qmz 2qr2 2qwx 2qx4 2qx6 2qx8 2qx9 3fw1 3g5m 3gam 3nfr 3nhf 3nhj 3nhk 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 4xdh 4zvk 4zvl 4zvm 4zvn 5buc 5lbt 5lbu

(-) Related Entries Specified in the PDB File

3g5m CASIMIROIN ANALOG
3gam CASIMIROIN ANALOG
3nhf
3nhj
3nhk
3nhp
3nhr
3nhs
3nhu
3nhw
3nhy