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(-) Description

Title :  CRYSTAL STRUCTURE OF KEAP1 IN COMPLEX WITH SYNTHETIC SMALL MOLECULAR BASED ON A CO-CRYSTALLIZATION
 
Authors :  N. Kunishima, T. Tanaka, M. Satoh, H. Saburi
Date :  12 Jan 12  (Deposition) - 16 Jan 13  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Small Molecular Complex, Beta-Propeller, Kelch Repeat Motif, Soaking, Stress Sensor, Small Molecular Binding, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Kunishima, T. Tanaka, M. Satoh, H. Saburi
Crystal Structure Of Keap1 In Complex With Synthetic Small Molecular Based On A Co-Crystallization
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTA2
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 321-609
    GeneKEAP1, INRF2, KIAA0132, KLHL19
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYTOSOLIC INHIBITOR OF NRF2, INRF2, KELCH-LIKE PROTEIN 19

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FUU1Ligand/Ion2-(3-((3-(5-(FURAN-2-YL)-1,3,4-OXADIAZOL-2-YL)UREIDO)METHYL)PHENOXY)ACETIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:13 , ARG A:15 , SER A:42 , ARG A:59 , ASN A:61 , HIS A:195 , ARG A:215 , PHE A:256 , PRO A:265 , ASP A:266 , HOH A:413 , HOH A:424 , HOH A:433 , HOH A:575 , HOH A:595BINDING SITE FOR RESIDUE FUU A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VNG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032105G333CKEAP1_HUMANUnclassified  ---AG12C
2UniProtVAR_032106D349NKEAP1_HUMANPolymorphism1048289AD28N
3UniProtVAR_032107G350SKEAP1_HUMANPolymorphism777308626AG29S
4UniProtVAR_032108G364CKEAP1_HUMANUnclassified  ---AG43C
5UniProtVAR_032109G430CKEAP1_HUMANUnclassified  ---AG109C
6UniProtVAR_036085A522VKEAP1_HUMANUnclassified  ---AA201V

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003936232ENSE00001516066chr19:10613481-10613373109KEAP1_HUMAN-00--
1.3ENST000003936233ENSE00001217274chr19:10610756-10610071686KEAP1_HUMAN1-2132130--
1.4ENST000003936234ENSE00001217262chr19:10602938-10602253686KEAP1_HUMAN214-4422291A:1-121121
1.5ENST000003936235ENSE00000679299chr19:10600529-10600324206KEAP1_HUMAN442-511701A:121-19070
1.6ENST000003936236ENSE00000679301chr19:10600044-10599868177KEAP1_HUMAN511-570601A:190-24960
1.7ENST000003936237ENSE00001371225chr19:10597494-10596796699KEAP1_HUMAN570-624551A:249-28840

(-) 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:288
 aligned with KEAP1_HUMAN | Q14145 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:288
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601        
          KEAP1_HUMAN   322 PKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRMITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVETETWTFVAPMKHRRSALGITVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT 609
               SCOP domains d3vnga_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee..........eeee......eee...........eeeee..eeeee..eeee..eeee...eeeee....eeee...........eeeee..eeeee..ee..ee...eeee......eeee..........eeeee..eeeeeeee....eeeeeeee......eeee..........eeeee..eeeeeeee....eeeeeeeee....eeeee..........eeeee..eeeeeeee....eeeeeeeee....eeeeeee........eeee. Sec.struct. author
                 SAPs(SNPs) -----------C---------------NS-------------C-----------------------------------------------------------------C-------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:1-121 UniProt: 214-442 [INCOMPLETE]                                                                     --------------------------------------------------------------------Exon 1.6  PDB: A:190-249 UniProt: 511-570                   --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:121-190 UniProt: 442-511                             ----------------------------------------------------------Exon 1.7  PDB: A:249-288 [INCOMPLETE]    Transcript 1 (2)
                 3vng A   1 PKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRMITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVETETWTFVAPMKHRRSALGITVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KEAP1_HUMAN | Q14145)
molecular function
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0019694    alkanesulfonate metabolic process    The chemical reactions and pathways involving alkanesulfonates, the anion of alkanesulfonic acids, sulfonic acid derivatives containing an aliphatic hydrocarbon group.
    GO:0071353    cellular response to interleukin-4    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-4 stimulus.
    GO:0071407    cellular response to organic cyclic compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0042994    cytoplasmic sequestering of transcription factor    The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
    GO:0009812    flavonoid metabolic process    The chemical reactions and pathways involving flavonoids, a group of water-soluble phenolic derivatives containing a flavan skeleton including flavones, flavonols and flavanoids, and anthocyanins.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0006108    malate metabolic process    The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0010499    proteasomal ubiquitin-independent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome but do not involve ubiquitin.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0045604    regulation of epidermal cell differentiation    Any process that modulates the frequency, rate or extent of epidermal cell differentiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035902    response to immobilization stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of being rendered immobile.
    GO:0010038    response to metal ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
    GO:0097066    response to thyroid hormone    A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
    GO:0001887    selenium compound metabolic process    The chemical reactions and pathways involving compounds that contain selenium, such as selenocysteine.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0031463    Cul3-RING ubiquitin ligase complex    A ubiquitin ligase complex in which a cullin from the Cul3 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a BTB-domain-containing protein.
    GO:0005884    actin filament    A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
    GO:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KEAP1_HUMAN | Q141451u6d 1zgk 2flu 3vnh 3zgc 3zgd 4cxi 4cxj 4cxt 4ifj 4ifl 4ifn 4in4 4iqk 4l7b 4l7c 4l7d 4n1b 4xmb 5dad 5daf 5f72 5git 5nlb 5x54

(-) Related Entries Specified in the PDB File

3vnh