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(-) Description

Title :  STRUCTURE OF THE HUMAN DDX6 C-TERMINAL DOMAIN IN COMPLEX WITH AN EDC3-FDF PEPTIDE
 
Authors :  F. Tritschler, O. Weichenrieder
Date :  18 Feb 09  (Deposition) - 24 Mar 09  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dead-Box Protein, Nucleotide-Binding, P54, Rck, Mirna, P-Bodies, Helicase, Decapping, Rna-Binding, Proto-Oncogene, Phosphoprotein, Chromosomal Rearrangement, Atp-Dependent Rna Helicase, Hydrolase, Cytoplasm, Mrna Decay, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Tritschler, J. E. Braun, A. Eulalio, V. Truffault, E. Izaurralde, O. Weichenrieder
Structural Basis For The Mutually Exclusive Anchoring Of P Body Components Edc3 And Tral To The Dead Box Protein Ddx6/Me31B.
Mol. Cell V. 33 661 2009
PubMed-ID: 19285948  |  Reference-DOI: 10.1016/J.MOLCEL.2009.02.014

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX6
    ChainsA, C
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSFDUET-1
    Expression System StrainROSETTA2(DE3)
    Expression System Taxid562
    FragmentC-TERMINAL DOMAIN, RESIDUES 296-483
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUMAN DDX6, DEAD BOX PROTEIN 6, ATP-DEPENDENT RNA HELICASE P54, ONCOGENE RCK
 
Molecule 2 - ENHANCER OF MRNA-DECAPPING PROTEIN 3
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSFDUET-1
    Expression System StrainROSETTA2(DE3)
    Expression System Taxid562
    FragmentFDF PEPTIDE, RESIDUES 192-228
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUMAN EDC3, LSM16 HOMOLOG, YJEF DOMAIN-CONTAINING PROTEIN 1, YJEF N-TERMINAL DOMAIN-CONTAINING PROTEIN 2, YJEF_N2, HYJEF_N2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CXS6Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CXS3Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CXS3Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:363 , PHE A:383 , ARG C:432 , PHE C:433 , TYR D:225 , HOH D:2024 , HOH D:2028 , HOH D:2029BINDING SITE FOR RESIDUE CXS D1227
02AC2SOFTWAREPRO A:450 , SER A:451 , PO4 B:1227BINDING SITE FOR RESIDUE CXS A1463
03AC3SOFTWAREGLU C:307 , ARG C:335 , LEU C:339BINDING SITE FOR RESIDUE CXS C1462
04AC4SOFTWAREARG A:308 , LEU A:339 , HOH A:2009 , HOH A:2100BINDING SITE FOR RESIDUE CXS A1464
05AC5SOFTWAREPHE A:318 , SER A:319 , LEU A:321 , ARG A:375 , HOH A:2015 , CXS C:1463BINDING SITE FOR RESIDUE CXS A1465
06AC6SOFTWARELEU A:346 , TYR A:348 , CXS A:1465 , PHE C:318 , SER C:319 , LEU C:321 , GLN C:322 , TYR C:348 , ARG C:375 , HOH C:2077 , HOH C:2078BINDING SITE FOR RESIDUE CXS C1463
07AC7SOFTWAREARG A:370 , ASP A:388 , GLN A:390 , HOH A:2101BINDING SITE FOR RESIDUE PO4 A1466
08AC8SOFTWARESER C:332 , SER C:333 , HOH C:2079BINDING SITE FOR RESIDUE PO4 C1464
09AC9SOFTWARESER A:332 , SER A:333 , LYS A:356 , HOH A:2102 , HOH A:2103BINDING SITE FOR RESIDUE PO4 A1467
10BC1SOFTWARESER A:451 , CXS A:1463 , HOH A:2085 , ASP B:205 , PHE B:206 , GLU B:207 , HOH B:2024BINDING SITE FOR RESIDUE PO4 B1227

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WAX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:412 -Arg A:413

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WAX)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003151271ENSE00001292931chr15:74988384-74988221164EDC3_HUMAN-00--
1.2bENST000003151272bENSE00001253727chr15:74967483-74967302182EDC3_HUMAN1-55550--
1.3ENST000003151273ENSE00001253676chr15:74964115-74963796320EDC3_HUMAN55-1621080--
1.4ENST000003151274ENSE00001253669chr15:74948409-74948074336EDC3_HUMAN162-2741132B:197-226
D:199-226
30
28
1.5ENST000003151275ENSE00001253663chr15:74932960-74932807154EDC3_HUMAN274-325520--
1.6ENST000003151276ENSE00001253655chr15:74927967-74927750218EDC3_HUMAN325-398740--
1.7bENST000003151277bENSE00001856853chr15:74925287-749228992389EDC3_HUMAN398-5081110--

(-) 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:161
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:166
                                   317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467      
           DDX6_HUMAN   308 GVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEY 473
               SCOP domains d2waxa_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains 2waxA00 A:297-462 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh....eeee............eeeeee.....hhhhhhhhhh..-----.eeeeeeehhhhhhhhhhhhhhhh...ee.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wax A 297 GVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRS-----LGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEY 462
                                   306       316       326       336       346       356       366       376       386       396       406       | -   |   426       436       446       456      
                                                                                                                                               414   420                                          

Chain B from PDB  Type:PROTEIN  Length:30
 aligned with EDC3_HUMAN | Q96F86 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:30
                                   206       216       226
           EDC3_HUMAN   197 EEIPDTDFDFEGNLALFDKAAVFEEIDTYE 226
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
               Transcript 1 Exon 1.4  PDB: B:197-226       Transcript 1
                 2wax B 197 EEIPDTDFDFEGNLALFDKAAVFEEIDTYE 226
                                   206       216       226

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with DDX6_HUMAN | P26196 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:166
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466      
           DDX6_HUMAN   307 KGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAE 472
               SCOP domains d2waxc_ C: automated matches                                                                                                                                           SCOP domains
               CATH domains 2waxC00 C:296-461 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
           Pfam domains (1) ---------------------------------------------Helicase_C-2waxC01 C:341-418                                                  ------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------Helicase_C-2waxC02 C:341-418                                                  ------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee.hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhh....eeee............eeeeee.....hhhhhhhhh.-........eeeeeehhhhhhhhhhhhhhhh...ee.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wax C 296 KGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIG-SGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAE 461
                                   305       315       325       335       345       355       365       375       385       395       405      |415       425       435       445       455      
                                                                                                                                              412 |                                               
                                                                                                                                                414                                               

Chain D from PDB  Type:PROTEIN  Length:28
 aligned with EDC3_HUMAN | Q96F86 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:28
                                   208       218        
           EDC3_HUMAN   199 IPDTDFDFEGNLALFDKAAVFEEIDTYE 226
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
           Pfam domains (1) FDF-2waxD01 D:199-226        Pfam domains (1)
           Pfam domains (2) FDF-2waxD02 D:199-226        Pfam domains (2)
         Sec.struct. author ......hhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
               Transcript 1 Exon 1.4  PDB: D:199-226     Transcript 1
                 2wax D 199 IPDTDFDFEGNLALFDKAAVFEEIDTYE 226
                                   208       218        

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Family: FDF (2)
2aFDF-2waxD01D:199-226
2bFDF-2waxD02D:199-226

(-) Gene Ontology  (29, 37)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (DDX6_HUMAN | P26196)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    GO:0033962    cytoplasmic mRNA processing body assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0043928    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
    GO:0019074    viral RNA genome packaging    The packaging of viral RNA (single-stranded or double-stranded) into a nucleocapsid.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0016442    RISC complex    A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    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: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.

Chain B,D   (EDC3_HUMAN | Q96F86)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:1990174    phosphodiesterase decapping endonuclease activity    Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA.
    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:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0033962    cytoplasmic mRNA processing body assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0031087    deadenylation-independent decapping of nuclear-transcribed mRNA    Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.
    GO:0043928    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX6_HUMAN | P261961vec 2way 4crw 4ct4 4ct5 5anr
        EDC3_HUMAN | Q96F862vc8 2way 3d3j 3d3k

(-) Related Entries Specified in the PDB File

1vec CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF RCK/P54, AHUMAN DEAD-BOX PROTEIN
2vc8 CRYSTAL STRUCTURE OF THE LSM DOMAIN OF HUMAN EDC3 (ENHANCER OF DECAPPING 3)
2way STRUCTURE OF THE HUMAN DDX6 C-TERMINAL DOMAIN IN COMPLEX WITH AN EDC3-FDF PEPTIDE