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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN DPF2 TANDEM PHD FINGER DOMAIN
 
Authors :  F. M. Huber, A. M. Davenport, A. Hoelz
Date :  01 Apr 17  (Deposition) - 24 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone Reader, Tandem Phd Finger, Aml, Myeloid Differentiation, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. M. Huber, S. M. Greenblatt, A. M. Davenport, C. Martinez, Y. Xu, L. P. Vu, S. D. Nimer, A. Hoelz
Histone-Binding Of Dpf2 Mediates Its Repressive Role In Myeloid Differentiation.
Proc. Natl. Acad. Sci. V. 114 6016 2017 U. S. A.
PubMed-ID: 28533407  |  Reference-DOI: 10.1073/PNAS.1700328114

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN UBI-D4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentDPF2 TANDEM PHD FINGER DOMAIN (UNP RESIDUES 270-391)
    GeneDPF2, BAF45D, REQ, UBID4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPOPTOSIS RESPONSE ZINC FINGER PROTEIN,BRG1-ASSOCIATED FACTOR 45D,BAF45D,D4,ZINC AND DOUBLE PHD FINGERS FAMILY 2,PROTEIN REQUIEM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:4 , CYS A:7 , HIS A:34 , CYS A:37binding site for residue ZN A 201
2AC2SOFTWARECYS A:26 , CYS A:29 , CYS A:55 , CYS A:58binding site for residue ZN A 202
3AC3SOFTWARECYS A:76 , CYS A:79 , CYS A:102 , CYS A:105binding site for residue ZN A 203
4AC4SOFTWARECYS A:61 , CYS A:64 , HIS A:84 , CYS A:87binding site for residue ZN A 204
5AC5SOFTWAREPHE A:6 , CYS A:55 , ILE A:56 , HOH A:310 , HOH A:317binding site for residue GOL A 205
6AC6SOFTWAREPRO A:90 , SER A:91binding site for residue GOL A 206
7AC7SOFTWAREILE A:63 , HIS A:103 , LEU A:104 , HOH A:301 , HOH A:306 , HOH A:308 , HOH A:314 , HOH A:350 , HOH A:351binding site for residue EDO A 207
8AC8SOFTWAREARG A:52 , GLN A:54 , CYS A:61 , ASN A:62 , HOH A:312 , HOH A:373binding site for residue EDO A 208
9AC9SOFTWAREGLY A:98 , SER A:99 , SER A:114 , ILE A:115 , TYR A:116 , GLN A:117 , HOH A:302binding site for residue EDO A 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:89 -Pro A:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5VDC)

(-) Sequences/Alignments

Asymmetric/Biological 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................ee......ee.......hhhhhhhh....................hhh.eee......eee.................hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5vdc A   1 NNYCDFCLGDSKINKKTGQPEELVSCSDCGRSGHPSCLQFTPVMMAAVKTYRWQCIECKCCNICGTSENDDQLLFCDDCDRGYHMYCLTPSMSEPPEGSWSCHLCLDLLKEKASIYQ 117
                                    10        20        30        40        50        60        70        80        90       100       110       

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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 5VDC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        REQU_HUMAN | Q927853iuf 5b79

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