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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DDX41 DEAD DOMAIN IN COMPLEX WITH SO42- AND MG2+
 
Authors :  Y. Jiang, S. Ouyang, Z. J. Liu
Date :  13 Oct 16  (Deposition) - 18 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Sensor Cdns Receptor Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Jiang, Y. Zhu, W. Qiu, Y. J. Liu, G. Cheng, Z. J. Liu, S. Ouyang
Structural And Functional Analyses Of Human Ddx41 Dead Domain
Protein Cell V. 8 72 2017
PubMed-ID: 27928732  |  Reference-DOI: 10.1007/S13238-016-0351-9

(-) Compounds

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX41
    ChainsA, B
    EC Number3.6.4.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPARG4
    Expression System Taxid1182032
    Expression System VectorPPPARG4
    FragmentUNP RESIDUES 153-410
    GeneDDX41, ABS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDEAD BOX PROTEIN 41,DEAD BOX PROTEIN ABSTRAKT HOMOLOG

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:228 , SER A:229 , GLY A:230 , LYS A:231 , THR A:232 , HOH A:624binding site for residue SO4 A 501
2AC2SOFTWARETHR A:227 , LYS A:231 , GLU A:345 , HOH A:624binding site for residue MG A 502
3AC3SOFTWAREGLY B:228 , SER B:229 , GLY B:230 , LYS B:231 , THR B:232 , HOH B:661binding site for residue SO4 B 501
4AC4SOFTWARETHR B:227 , LYS B:231 , GLU B:345 , HOH B:661binding site for residue MG B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H1Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H1Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5H1Y)

(-) 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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eee................hhhhhhhhhh......hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh....eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h1y A 157 EERHERVRKKYHILVEGDGIPPPIKSFKEMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINV 398
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396  

Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eee................hhhhhhhhhh......hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h1y B 154 SMSEERHERVRKKYHILVEGDGIPPPIKSFKEMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINV 398
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     

   Legend:   → Mismatch (orange background)
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  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 5H1Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H1Y)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDX41_HUMAN | Q9UJV92p6n 5gvr 5gvs

(-) Related Entries Specified in the PDB File

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