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(-) Description

Title :  CRYSTAL STRUCTURE OF LOV1 DOMAIN OF PHOTOTROPIN1 FROM ARABIDOPSIS THALIANA
 
Authors :  M. Nakasako, D. Matsuoka, S. Tokutomi
Date :  29 Jul 07  (Deposition) - 29 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pas-Fold, Lov-Fold, Atp-Binding, Chromophore, Cytoplasm, Flavoprotein, Fmn, Kinase, Membrane, Nucleotide-Binding, Phosphorylation, Photoreceptor Protein, Receptor, Sensory Transduction, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Nakasako, K. Zikihara, D. Matsuoka, H. Katsura, S. Tokutomi
Structural Basis Of The Lov1 Dimerization Of Arabidopsis Phototropins 1 And 2
J. Mol. Biol. V. 381 718 2008
PubMed-ID: 18585389  |  Reference-DOI: 10.1016/J.JMB.2008.06.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOTOTROPIN-1
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 180-308, LOV1 DOMAIN
    GenePHOT1, JK224, NPH1, RPT1
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymNON-PHOTOTROPIC HYPOCOTYL PROTEIN 1, ROOT PHOTOTROPISM PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:202 , ASN A:233 , CYS A:234 , ARG A:235 , LEU A:237 , GLN A:238 , LEU A:247 , ILE A:250 , ARG A:251 , LEU A:254 , ILE A:264 , ASN A:266 , ASN A:276 , LEU A:278 , PHE A:293 , GLY A:295 , GLN A:297BINDING SITE FOR RESIDUE FMN A 500
2AC2SOFTWARESER B:202 , ASN B:233 , CYS B:234 , ARG B:235 , LEU B:237 , GLN B:238 , LEU B:247 , ARG B:251 , LEU B:254 , ILE B:264 , ASN B:266 , ASN B:276 , LEU B:278 , PHE B:293 , GLY B:295 , GLN B:297BINDING SITE FOR RESIDUE FMN B 500

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:261 -B:261

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z6C)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.PHOT1_ARATH184-233
 
466-535
  2A:184-233
B:184-233
-
2PACPS50113 PAC domain profile.PHOT1_ARATH258-312
 
536-590
  2A:258-304
B:258-304
-

(-) Exons   (0, 0)

(no "Exon" information available for 2Z6C)

(-) 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:121
 aligned with PHOT1_ARATH | O48963 from UniProtKB/Swiss-Prot  Length:996

    Alignment length:121
                                   193       203       213       223       233       243       253       263       273       283       293       303 
          PHOT1_ARATH   184 VSEDLKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADELAKIRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPIKDESGKVLKFIGMQVEVSKHT 304
               SCOP domains d2z6ca_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....eeeeeee.......eeee..hhhhhhh.........hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PAS  PDB: A:184-233 UniProt: 184-233              ------------------------PAC  PDB: A:258-304 UniProt: 258-312            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z6c A 184 VSEDLKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADELAKIRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPIKDESGKVLKFIGMQVEVSKHT 304
                                   193       203       213       223       233       243       253       263       273       283       293       303 

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PHOT1_ARATH | O48963 from UniProtKB/Swiss-Prot  Length:996

    Alignment length:121
                                   193       203       213       223       233       243       253       263       273       283       293       303 
          PHOT1_ARATH   184 VSEDLKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADELAKIRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPIKDESGKVLKFIGMQVEVSKHT 304
               SCOP domains d2z6cb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------PAS_9-2z6cB01 B:199-302                                                                                 -- Pfam domains (1)
           Pfam domains (2) ---------------PAS_9-2z6cB02 B:199-302                                                                                 -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh..eeeeee.......eeee.hhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PAS  PDB: B:184-233 UniProt: 184-233              ------------------------PAC  PDB: B:258-304 UniProt: 258-312            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z6c B 184 VSEDLKDALSTFQQTFVVSDATKPDYPIMYASAGFFNMTGYTSKEVVGRNCRFLQGSGTDADELAKIRETLAAGNNYCGRILNYKKDGTSFWNLLTIAPIKDESGKVLKFIGMQVEVSKHT 304
                                   193       203       213       223       233       243       253       263       273       283       293       303 

   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 2Z6C)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PHOT1_ARATH | O48963)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0009882    blue light photoreceptor activity    The function of absorbing and responding to electromagnetic radiation with a wavelength of approximately 400-470nm. The response may involve a change in conformation.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    GO:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009785    blue light signaling pathway    The series of molecular signals initiated upon sensing of blue light by photoreceptor molecule, at a wavelength between 400nm and 470nm.
    GO:0009904    chloroplast accumulation movement    The relocation process in which chloroplasts in photosynthetic cells move toward a brighter area in a cell to optimize photosynthesis.
    GO:0009903    chloroplast avoidance movement    The relocation process in which chloroplasts in photosynthetic cells avoid strong light and move away from it in order to preserve the photosynthetic machinery.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0010362    negative regulation of anion channel activity by blue light    Any process in which blue light stops, prevents, or reduces the frequency, rate, or extent of the anion channel activity.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009638    phototropism    The movement of an organism, or part of an organism, in response to a light stimulus, usually toward or away from it.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    GO:0010155    regulation of proton transport    Any process that modulates the frequency, rate or extent of proton transport into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010119    regulation of stomatal movement    Any process that modulates the frequency, rate or extent of stomatal movement.
    GO:0009637    response to blue light    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 blue light stimulus. Blue light is electromagnetic radiation with a wavelength of between 440 and 500nm.
    GO:0050896    response to stimulus    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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHOT1_ARATH | O489634hhd

(-) Related Entries Specified in the PDB File

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