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(-) Description

Title :  CRYSTAL STRUCTURE OF INSULYSIN WITH BOUND ATP
 
Authors :  D. W. Rodgers, N. Noinaj
Date :  19 Sep 11  (Deposition) - 26 Oct 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thermolysin-Like Fold Active Site Region, Hydrolyase, Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Noinaj, E. S. Song, S. Bhasin, B. J. Alper, W. K. Schmidt, L. B. Hersh, D. W. Rodgers
Anion Activation Site Of Insulin-Degrading Enzyme.
J. Biol. Chem. V. 287 48 2012
PubMed-ID: 22049080  |  Reference-DOI: 10.1074/JBC.M111.264614

(-) Compounds

Molecule 1 - INSULIN-DEGRADING ENZYME
    ChainsA
    EC Number3.4.24.56
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System StrainSF9
    Expression System Taxid7108
    FragmentUNP RESIDUES 1-1019
    GeneIDE
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymINSULIN PROTEASE, INSULINASE, INSULYSIN
 
Molecule 2 - PEPTIDE
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System StrainSF9
    Expression System Taxid7108
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    Other DetailsPEPTIDE LIKELY CLEAVAGE PRODUCT FROM POLYHISTIDINE TAG

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2UNK3Mod. Amino Acid

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:429 , ASP A:895 , LYS A:896 , PRO A:897 , LYS A:898 , LYS A:899 , SER A:901 , ALA A:902 , ALA A:905BINDING SITE FOR RESIDUE ATP A 1020

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TUV)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INSULINASEPS00143 Insulinase family, zinc-binding region signature.IDE_RAT95-118  1A:95-118

(-) Exons   (0, 0)

(no "Exon" information available for 3TUV)

(-) 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:961
 aligned with IDE_RAT | P35559 from UniProtKB/Swiss-Prot  Length:1019

    Alignment length:970
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       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       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011
             IDE_RAT     42 MNNPAIQRIEDHIVKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIPGLSHFCEHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRFAQFFLCPLFDASCKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVREELLKFHSTYYSSNLMAICVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQQYYKSNPGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEGPQEWVFQECKDLNAVAFRFKDKERPRGYTSKIAGKLHYYPLNGVLTAEYLLEEFRPDLIDMVLDKLRPENVRVAIVSKSFEGKTDRTEQWYGTQYKQEAIPEDVIQKWQNADLNGKFKLPTKNEFIPTNFEILALEKDATPYPALIKDTAMSKLWFKQDDKFFLPKACLNFEFFSPFAYVDPLHCNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKITEKMATFEIDKKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGVMQMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQRRNEVHNNCGIEIYYQTDMQSTSENMFLELFCQIISEPCFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKAIEDMTEEAFQKHIQALAIRRLDKPKKLSAECAKYWGEIISQQYNYDRDNIEVAYLKTLSKDDIIKFYKEMLAVDAPRRHKVSVHVLAREMDSCPVVGEFPSQNDINLSEAPPLPQPEVIHNMTEFKRGLPLFPLVKPH 1011
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........eeeeeee....eeeeee.....eeeeeeee..hhhhh.....hhhhhhhhhhh.........hhhhhhhhh...eeeeee....eeeeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhh....hhhhhh.hhhhhh.hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhh.................hhhhh.eeeee.......eeeeeeeee.hhhhh..hhhhhhhhhhh.....hhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhh..........hhhhhhhhhhhhhhhh.eeeee.hhhh....ee......eeeeee.hhhhhhhhhh.................................eeeee...eeeeeee.......eeeeeeeee.hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..ee.hhhhh............eeeeeee......eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhh.......eeeeeeee.........---------............eee.hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------INSULINASE  PDB: A:95-11----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3tuv A   42 MNNPAIQRIEDHIVKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDVHIGSLSDPPNIPGLSHFCEHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNYYFDVSHEHLEGALDRFAQFFLCPLFDASCKDREVNAVDSEHEKNVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVREELLKFHSTYYSSNLMAICVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQQYYKSNPGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIILHMFQYIQKLRAEGPQEWVFQECKDLNAVAFRFKDKERPRGYTSKIAGKLHYYPLNGVLTAEYLLEEFRPDLIDMVLDKLRPENVRVAIVSKSFEGKTDRTEQWYGTQYKQEAIPEDVIQKWQNADLNGKFKLPTKNEFIPTNFEILALEKDATPYPALIKDTAMSKLWFKQDDKFFLPKACLNFEFFSPFAYVDPLHCNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILLKKITEKMATFEIDKKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGVMQMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQRRNEVHNNCGIEIYYQTDMQSTSENMFLELFCQIISEPCFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLITMEKAIEDMTEEAFQKHIQALAIRRLDKPKKLSAECAKYWGEIISQQYNYDRDNIEVAYLKTLSKDDIIKFYKEMLAVDAPRRHKVSVHVLAREMDSCPV---------INLSEAPPLPQPEVIHNMTEFKRGLPLFPLVKPH 1011
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       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       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961      |  -      |981       991      1001      1011
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        968       978                                 

Chain B from PDB  Type:PROTEIN  Length:3
                                    
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                3tuv B    1 xxx    3
                            |||
                            1-UNK
                             2-UNK
                              3-UNK

   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 3TUV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IDE_RAT | P35559)
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:0001540    amyloid-beta binding    Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
    GO:0031626    beta-endorphin binding    Interacting selectively and non-covalently with beta-endorphin, a peptide generated by the cleavage of pro-opiomelanocortin.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0043559    insulin binding    Interacting selectively and non-covalently with insulin, a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0017046    peptide hormone binding    Interacting selectively and non-covalently with any peptide with hormonal activity in animals.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0050435    amyloid-beta metabolic process    The chemical reactions and pathways involving amyloid-beta, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP).
    GO:0010815    bradykinin catabolic process    The chemical reactions and pathways resulting in the breakdown of the peptide bradykinin.
    GO:0044257    cellular protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0042447    hormone catabolic process    The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
    GO:1901143    insulin catabolic process    The chemical reactions and pathways resulting in the breakdown of insulin.
    GO:1901142    insulin metabolic process    The chemical reactions and pathways involving insulin.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0043171    peptide catabolic process    The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    GO:0051291    protein heterooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:0010992    ubiquitin recycling    Any process involved in the maintenance of an internal steady state of ubiquitin monomers and free ubiquitin chains at the level of the cell by recycling ubiquitin from proteasome-bound ubiquitinated intermediates.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031597    cytosolic proteasome complex    A proteasome complex found in the cytosol of a cell.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IDE_RAT | P355593p7l 3p7o

(-) Related Entries Specified in the PDB File

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