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(-) Description

Title :  CRYSTAL STRUCTURE OF NA,K-ATPASE N-DOMAIN
 
Authors :  K. O. Hakansson
Date :  30 Jul 03  (Deposition) - 03 Aug 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Anti-Parallel Beta Sheet, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. O. Hakansson
The Crystallographic Structure Of Na, K-Atpase N-Domain At 2. 6 A Resolution
J. Mol. Biol. V. 332 1175 2003
PubMed-ID: 14499619  |  Reference-DOI: 10.1016/J.JMB.2003.07.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NA,K-ATPASE
    ChainsA
    EC Number3.6.3.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-40
    Expression System StrainXL1-BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-DOMAIN, OR NUCLEOTIDE BINDING DOMAIN
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:590 , HIS A:592BINDING SITE FOR RESIDUE NI A 601
2AC2SOFTWAREHOH A:81 , HIS A:383 , GLU A:392 , HIS A:588 , HIS A:591BINDING SITE FOR RESIDUE NI A 602
3AC3SOFTWAREHIS A:587 , HIS A:589BINDING SITE FOR RESIDUE NI A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q3I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q3I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q3I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q3I)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q3I)

(-) Sequences/Alignments

Asymmetric 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:192
 aligned with AT1A2_PIG | D2WKD8 from UniProtKB/Swiss-Prot  Length:1020

    Alignment length:214
                                   392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592    
            AT1A2_PIG   383 RMTVAHMWFDNQIHEADTTEDQSGATFDKRSPTWTALSRIAGLCNRAVFKAGQENISVSKRDTAGDASESALLKCIELSCGSVRKMRDRNPKVAEIPFNSTNKYQLSIHEREDNPQSHVLVMKGAPERILDRCSSILVQGKEIPLDKEMQDAFQNAYLELGGLGERVLGFCQLNLPSGKFPRGFKFDTDELNFPTEKLCFVGLMSMIDPPRAAV 596
               SCOP domains d1q3ia_ A: Sodium/p      otassium-transporting AT          Pase alpha chain                                                                                                                                            SCOP domains
               CATH domains 1q3iA00 A:378-592 C      alcium-transporting ATPa          se, cytoplasmic domain N                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeee....------.....hhhhhhhhhhhhhh.....----------......hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.------.eeeeee.......eeeeeeehhhhhhhheeeeee..eeee.hhhhhhhhhhhhhhhhhh..eeeeeeeeee......................eeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q3i A 378 MMTVAHMWFDNQIHEADTT------TFDKRSPTWTALSRIAGLCNRAVF----------KRDTAGDASESALLKCIELSCGSVRKMRDRNPKVAEIS------YQLSIHEREDNPQSHVLVMKGAPERILDRCSSILVQGKEIPLDKEMQDAFQNAYLELGGLGERVLGFCQLNLPSGKFPRGFKFDTDELNFPTEKLCFVGLMSMIDHHHHHH 592
                                   387        |-     | 407       417    ||  |-       437       447       457       467      |  -   |   487  ||   498       508       518       528       538       548       558       568       578       588    
                                            396    403                422|  |        437                                  474    481      490|                                                                                                    
                                                                       424  |                                                              492                                                                                                    
                                                                          427                                                                                                                                                                     

   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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q3I)

(-) Gene Ontology  (50, 50)

Asymmetric Unit(hide GO term definitions)
Chain A   (AT1A2_PIG | D2WKD8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
    GO:0031402    sodium ion binding    Interacting selectively and non-covalently with sodium ions (Na+).
    GO:0005391    sodium:potassium-exchanging ATPase activity    Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) + K+(out) = ADP + phosphate + Na+(out) + K+(in).
    GO:1990239    steroid hormone binding    Interacting selectively and non-covalently with a steroid hormone.
biological process
    GO:0015991    ATP hydrolysis coupled proton transport    The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis.
    GO:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    GO:0030007    cellular potassium ion homeostasis    Any process involved in the maintenance of an internal steady state of potassium ions at the level of a cell.
    GO:0071383    cellular response to steroid hormone stimulus    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 a steroid hormone stimulus.
    GO:0006883    cellular sodium ion homeostasis    Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell.
    GO:0010248    establishment or maintenance of transmembrane electrochemical gradient    The directed movement of ions to establish or maintain an electrochemical gradient across a membrane by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0040011    locomotion    Self-propelled movement of a cell or organism from one location to another.
    GO:0051481    negative regulation of cytosolic calcium ion concentration    Any process that decreases the concentration of calcium ions in the cytosol.
    GO:0045822    negative regulation of heart contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
    GO:0045988    negative regulation of striated muscle contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction.
    GO:0001504    neurotransmitter uptake    The directed movement of neurotransmitters into neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters.
    GO:0010107    potassium ion import    The directed movement of potassium ions into a cell or organelle.
    GO:0006813    potassium ion transport    The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0008217    regulation of blood pressure    Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
    GO:0006937    regulation of muscle contraction    Any process that modulates the frequency, rate or extent of muscle contraction.
    GO:0002087    regulation of respiratory gaseous exchange by neurological system process    A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates.
    GO:0006940    regulation of smooth muscle contraction    Any process that modulates the frequency, rate or extent of smooth muscle contraction.
    GO:0006942    regulation of striated muscle contraction    Any process that modulates the frequency, rate or extent of striated muscle contraction.
    GO:0002026    regulation of the force of heart contraction    Any process that modulates the extent of heart contraction, changing the force with which blood is propelled.
    GO:0019229    regulation of vasoconstriction    Any process that modulates the frequency, rate or extent of reductions in the diameter of blood vessels.
    GO:1903416    response to glycoside    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 glycoside stimulus.
    GO:0036376    sodium ion export from cell    The directed movement of sodium ions out of a cell.
    GO:0006814    sodium ion transport    The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0008542    visual learning    Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
    GO:0030315    T-tubule    Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
    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:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
    GO:0005890    sodium:potassium-exchanging ATPase complex    Sodium:potassium-exchanging ATPases are tetrameric proteins, consisting of two large alpha subunits and two smaller beta subunits. The alpha subunits bear the active site and penetrate the membrane, while the beta subunits carry oligosaccharide groups and face the cell exterior.

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