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(-) Description

Title :  HUMAN TDRD3 DUF1767-OB DOMAINS
 
Authors :  S. Goto-Ito, A. Yamagata, Y. Sato, T. S. Takahashi, S. Fukai
Date :  05 Sep 16  (Deposition) - 14 Jun 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Scaffold Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Goto-Ito, A. Yamagata, T. S. Takahashi, Y. Sato, S. Fukai
Structural Basis Of The Interaction Between Topoisomerase Iii Beta And The Tdrd3 Auxiliary Factor
Sci Rep V. 7 42123 2017
PubMed-ID: 28176834  |  Reference-DOI: 10.1038/SREP42123

(-) Compounds

Molecule 1 - TUDOR DOMAIN-CONTAINING PROTEIN 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-161
    GeneTDRD3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:-3 , PRO A:-2 , GLY A:-1 , HIS A:0 , HOH A:306 , HOH A:307 , HIS B:0 , GLN B:3 , GLU B:22 , EDO B:204 , HOH B:307binding site for residue PO4 A 201
2AC2SOFTWARESER A:27 , HOH A:305 , GLY B:-3 , HIS B:0 , GLU B:22 , THR B:25 , SER B:26 , SER B:27 , PRO B:28 , MG B:205 , HOH B:357binding site for residue PO4 B 201
3AC3SOFTWARELYS A:136 , LYS B:75 , ARG B:96 , GLN B:98 , GLU B:159binding site for residue EDO B 202
4AC4SOFTWARETRP B:14 , ILE B:37 , LYS B:160 , TRP B:161 , HOH B:315binding site for residue EDO B 203
5AC5SOFTWAREHIS A:0 , PO4 A:201 , HOH A:325 , GLN B:3 , HOH B:307 , HOH B:346binding site for residue EDO B 204
6AC6SOFTWARETHR B:25 , PO4 B:201 , HOH B:318 , HOH B:365binding site for residue MG B 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:67 -Pro A:68
2Gly B:67 -Pro B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GVD)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhh.hhhhhh..............eee..eeeeeeeee...eeeeeeee....eeeeeeee.............eeee..eeeee..eeeee...eeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gvd A  -3 GPGHMAQVAGAALSQAGWYLSDEGIEACTSSPDKVNVNDIILIALNTDLRTIGKKFLPSDINSGKVEKLEGPCVLQIQKIRNAPRMLRLQMTDGHISCTAVEFSYMSKISLNTPPGTKVKLSGIVDIKNGFLLLNDSNTTVLGGEVEHLIEKW 161
                                     6        16        26        36        46        56        66        76 ||     98       108       118       128       138       148       158   
                                                                                                            78|                                                                      
                                                                                                             91                                                                      

Chain B from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhh.hhhhhh..............eee..eeeeeeeeee....eeeeee....eeeeee...............eeee..eeeee..eeee....eeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gvd B  -3 GPGHMAQVAGAALSQAGWYLSDEGIEACTSSPDKVNVNDIILIALNTDLRTIGKKFLPSDINSGKVEKLEGPCVLQIQKIRNVARMLRLQMTDGHISCTAVEFSYMSKISLNTPPGTKVKLSGIVDIKNGFLLLNDSNTTVLGGEVEHLIEKW 161
                                     6        16        26        36        46        56        66        76   ||   98       108       118       128       138       148       158   
                                                                                                              80|                                                                    
                                                                                                               93                                                                    

   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 5GVD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDRD3_HUMAN | Q9H7E21wji 2lto 3pmt 3pnw 3s6w 5gve

(-) Related Entries Specified in the PDB File

5gvc 5gve