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(-) Description

Title :  ANTPHD WITH 15BP DNA DUPLEX R-MONOTHIOATED AT CYTIDINE-8
 
Authors :  M. A. White, L. Zandarashvili, J. Iwahara, D. Nguyen
Date :  27 Apr 16  (Deposition) - 22 Jun 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Homeodomain, Dna-Binding Protein, Complex (Homeodomain-Dna), Transcription-Dna Complex, Transcription Regulator-Dna Complex, Monothiolated Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nguyen, L. Zandarashvili, M. A. White, J. Iwahara
Stereospecific Effects Of Oxygen-To-Sulfur Substitution In Dna Phosphate On Ion Pair Dynamics And Protein-Dna Affinity
Chembiochem V. 17 1636 2016
PubMed-ID: 27271797  |  Reference-DOI: 10.1002/CBIC.201600265

(-) Compounds

Molecule 1 - HOMEOTIC PROTEIN ANTENNAPEDIA
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ANTP, CG1028
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7R) P*AP*TP*TP*AP*GP*AP*G)-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Other Details: R-MONOTHIOLATED PHOSPHATE AT CYTIDINE 8
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)- 3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1C7R2Mod. Nucleotide2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NI6Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1C7R1Mod. Nucleotide2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE
2MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1C7R1Mod. Nucleotide2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:21 , HOH A:206 , HIS D:21 , ASN D:60 , HOH D:114binding site for residue NI A 101
02AC2SOFTWAREDG B:1 , HOH C:122binding site for residue NI B 101
03AC3SOFTWAREDG B:12 , HOH B:207binding site for residue NI B 102
04AC4SOFTWAREDA B:3 , DA B:4 , DT C:13binding site for residue NI B 103
05AC5SOFTWAREDG E:2 , HOH E:205 , HOH E:218binding site for residue NI E 101
06AC6SOFTWAREDG E:13binding site for residue NI E 102
07AC7SOFTWAREDT F:13 , MPD F:102binding site for residue MPD F 101
08AC8SOFTWAREDT F:13 , MPD F:101 , MPD F:103binding site for residue MPD F 102
09AC9SOFTWAREDT F:14 , MPD F:102binding site for residue MPD F 103
10AD1SOFTWARETYR D:25 , GLN D:50 , ARG D:53 , MET D:54 , DG E:6 , DA E:9 , DG F:9 , DG F:10binding site for Di-nucleotide DC E 7 and C7R E 8
11AD2SOFTWAREMET D:54 , DC E:7 , DT E:10 , DA F:7 , DT F:8 , DG F:9 , DG F:10binding site for Di-nucleotide C7R E 8 and DA E 9

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JLW)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:57
                                                                                        
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  5jlw A  4 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 60
                                    13        23        33        43        53       


Chain B from PDB  Type:DNA  Length:15
                                              
                  5jlw B  0 AGAAAGCxATTAGAG 14
                                   | 9     
                                   7-C7R   


Chain C from PDB  Type:DNA  Length:15
                                              
                  5jlw C  0 TCTCTAATGGCTTTC 14
                                     9     


Chain D from PDB  Type:PROTEIN  Length:57
                                                                                        
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  5jlw D  4 GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 60
                                    13        23        33        43        53       


Chain E from PDB  Type:DNA  Length:15
                                              
                  5jlw E  1 AGAAAGCxATTAGAG 15
                                   |10     
                                   8-C7R   


Chain F from PDB  Type:DNA  Length:15
                                              
                  5jlw F  1 TCTCTAATGGCTTTC 15
                                    10
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  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 5JLW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANTP_DROME | P02833: 1ahd 1hom 1kz0 1kz5 1omq 1san 2hoa 2nd6 2nd7 2nd8 4xic 4xid 5jlx 9ant

(-) Related Entries Specified in the PDB File

5jlx