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(-) Description

Title :  ANTPHD WITH 15BP DI-THIOATE MODIFIED DNA DUPLEX
 
Authors :  M. A. White, L. Zandarashvili, J. Iwahara
Date :  06 Jan 15  (Deposition) - 25 Nov 15  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Dna Binding, Methylated Dna, Zinc Finger, Transcription, Transcription Regulator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Zandarashvili, D. Nguyen, K. M. Anderson, M. A. White, D. G. Gorenstein, J. Iwahara
Entropic Enhancement Of Protein-Dna Affinity By Oxygen-To-Sulfur Substitution In Dna Phosphate.
Biophys. J. V. 109 1026 2015
PubMed-ID: 26331260  |  Reference-DOI: 10.1016/J.BPJ.2015.07.032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMEOTIC PROTEIN ANTENNAPEDIA
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 297-356
    Gene: ANTP, CG1028
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S) P*AP*TP*TP*AP*GP*AP*G)-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    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, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1C2S2Mod. NucleotideCYTIDINE-5'-DITHIOPHOSPHORATE
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1C2S1Mod. NucleotideCYTIDINE-5'-DITHIOPHOSPHORATE
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1C2S1Mod. NucleotideCYTIDINE-5'-DITHIOPHOSPHORATE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG B:1 , HOH C:202binding site for residue NI B 101
2AC2SOFTWARETYR A:25 , DC C:37binding site for residue MPD C 101
3AC3SOFTWAREMPD F:101binding site for residue MPD D 101
4AC4SOFTWAREHIS A:21 , HIS D:21binding site for residue NI D 102
5AC5SOFTWAREDG E:1binding site for residue NI E 101
6AC6SOFTWAREMPD D:101 , DC F:37binding site for residue MPD F 101
7AC7SOFTWARETYR D:25 , GLN D:50 , ARG D:53 , MET D:54 , DG E:5 , DA E:8 , DG F:31 , DG F:32binding site for Di-nucleotide DC E 6 and C2S E 7
8AC8SOFTWAREMET D:54 , DC E:6 , DT E:9 , DA F:29 , DT F:30 , DG F:31 , DG F:32binding site for Di-nucleotide C2S E 7 and DA E 8

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XIC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XIC)

(-) 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:59
                                                                                          
               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
                  4xic A  2 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 60
                                    11        21        31        41        51         


Chain B from PDB  Type:DNA  Length:15
                                              
                  4xic B  0 AGAAAGCxATTAGAG 14
                                   | 9     
                                   7-C2S   


Chain C from PDB  Type:DNA  Length:15
                                              
                  4xic C 23 TCTCTAATGGCTTTC 37
                                    32     


Chain D from PDB  Type:PROTEIN  Length:56
                                                                                       
               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
                  4xic D  5 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 60
                                    14        24        34        44        54      


Chain E from PDB  Type:DNA  Length:15
                                              
                  4xic E  0 AGAAAGCxATTAGAG 14
                                   | 9     
                                   7-C2S   


Chain F from PDB  Type:DNA  Length:15
                                              
                  4xic F 23 TCTCTAATGGCTTTC 37
                                    32
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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 4XIC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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  4xic
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  ANTP_DROME | P02833
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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 4xid 5jlw 5jlx 9ant

(-) Related Entries Specified in the PDB File

4xid