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(-) Description

Title :  TBX5 DB, NKX2.5 HD, ANF DNA COMPLEX
 
Authors :  L. Pradhan
Date :  31 Dec 14  (Deposition) - 16 Dec 15  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Transcription Factor, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Pradhan, S. Gopal, S. Li, S. Ashur, S. Suryanarayanan, H. Kasahara, H. J. Nam
Intermolecular Interactions Of Cardiac Transcription Factor Nkx2. 5 And Tbx5.
Biochemistry V. 55 1702 2016
PubMed-ID: 26926761  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00171

(-) Compounds

Molecule 1 - T-BOX TRANSCRIPTION FACTOR TBX5
    Chains: A, E
    Engineered: YES
    Expression System: UNIDENTIFIED
    Expression System Taxid: 32644
    Fragment: DB (UNP RESIDUES 53-238)
    Gene: TBX5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: T-BOX PROTEIN 5
 
Molecule 2 - HOMEOBOX PROTEIN NKX-2.5
    Chains: B, F
    Engineered: YES
    Expression System: UNIDENTIFIED
    Expression System Taxid: 32644
    Fragment: HD (UNP RESIDUES 142-194)
    Gene: NKX2-5, CSX, NKX2.5, NKX2E
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARDIAC-SPECIFIC HOMEOBOX, HOMEOBOX PROTEIN CSX, HOMEOBOX PROTEIN NK-2 HOMOLOG E
 
Molecule 3 - 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP *G)-3'
    Chains: C, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: ANF DNA STRAND 1
    Synthetic: YES
 
Molecule 4 - 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP *A)-3'
    Chains: D, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: ANF DNA STRAND 2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4S0H)

(-) Sites  (0, 0)

(no "Site" information available for 4S0H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S0H)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Phe A:84 -Pro A:85
2Ala A:130 -Met A:131
3Ser A:141 -Pro A:142
4Phe E:84 -Pro E:85
5Ser E:141 -Pro E:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S0H)

(-) Exons   (0, 0)

(no "Exon" information available for 4S0H)

(-) 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhh...eee.....ee....eeeeee......eeeeeeeeee...eeeee....eeeeee.........ee.....eehhhhhhh.eee...eee.........ee.....eeeeeeeeee....eeee.hhhheeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s0h A  53 GIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKATAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRG 238
                                    62        72        82        92       102       112       122       132       142       152       162       172       182     ||202       212       222       232      
                                                                                                                                                                 188|                                       
                                                                                                                                                                  199                                       


Chain B from PDB  Type:PROTEIN  Length:53
                                                                                     
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 4s0h B 142 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 194
                                   151       161       171       181       191   


Chain C from PDB  Type:DNA  Length:19
                                                   
                 4s0h C   1 TCTCACACCTTTGAAGTGG  19
                                    10         


Chain D from PDB  Type:DNA  Length:19
                                                   
                 4s0h D   1 CCACTTCAAAGGTGTGAGA  19
                                    10         


Chain E from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhh.eee.....ee.....eeeee......eeeeeeeeeeeeeeeeee....eeeee..........ee.....eehhhhhh..ee....eee.........ee....eeeeeeeeee......eee.hhhhheeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s0h E  53 GIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRG 238
                                    62        72        82        92       102       112       122       132       142       152       162       172       182      |201       211       221       231       
                                                                                                                                                                  189|                                       
                                                                                                                                                                   199                                       


Chain F from PDB  Type:PROTEIN  Length:53
                                                                                     
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 4s0h F 105 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 157
                                   114       124       134       144       154   


Chain G from PDB  Type:DNA  Length:19
                                                   
                 4s0h G   1 TCTCACACCTTTGAAGTGG  19
                                    10         


Chain H from PDB  Type:DNA  Length:19
                                                   
                 4s0h H   1 CCACTTCAAAGGTGTGAGA  19
                                    10
   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 4S0H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S0H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S0H)

(-) Gene Ontology  (114, 132)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:130 - Met A:131   [ RasMol ]  
    Phe A:84 - Pro A:85   [ RasMol ]  
    Phe E:84 - Pro E:85   [ RasMol ]  
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  4s0h
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  NKX25_HUMAN | P52952
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  TBX5_HUMAN | Q99593
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 Related Entries

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

UniProtKB/Swiss-Prot
        NKX25_HUMAN | P52952: 3rkq
        TBX5_HUMAN | Q99593: 2x6u 2x6v 5bqd

(-) Related Entries Specified in the PDB File

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