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(-) Description

Title :  DPF3B IN COMPLEX WITH H3K14AC PEPTIDE
 
Authors :  W. Tempel, Y. Liu, J. R. Walker, A. Zhao, S. Qin, P. Loppnau, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genomics Consor (Sgc)
Date :  10 Feb 16  (Deposition) - 24 Feb 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Li, A. Zhao, W. Tempel, P. Loppnau, Y. Liu
Crystal Structure Of Dpf3B In Complex With An Acetylated Histone Peptide.
J. Struct. Biol. V. 195 365 2016
PubMed-ID: 27402533  |  Reference-DOI: 10.1016/J.JSB.2016.07.001

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN DPF3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 469008
    Gene: DPF3, BAF45C, CERD4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRG1-ASSOCIATED FACTOR 45C,BAF45C,ZINC FINGER PROTEIN CER- D4
 
Molecule 2 - H3K14AC PEPTIDE
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 43)

Asymmetric/Biological Unit (5, 43)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
4UNX32Ligand/IonUNKNOWN ATOM OR ION
5ZN8Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:262 , CYS A:265 , HIS A:292 , CYS A:295binding site for residue ZN A 1001
02AC2SOFTWARECYS A:284 , CYS A:287 , CYS A:313 , CYS A:316binding site for residue ZN A 1002
03AC3SOFTWARECYS A:319 , CYS A:322 , HIS A:342 , CYS A:345binding site for residue ZN A 1003
04AC4SOFTWARECYS A:334 , CYS A:337 , CYS A:360 , CYS A:363binding site for residue ZN A 1004
05AC5SOFTWARESER A:269 , GLU A:280 , THR A:303 , GLU A:304 , LYS A:307 , HOH A:1115binding site for residue EDO A 1005
06AC6SOFTWARECYS B:262 , CYS B:265 , HIS B:292 , CYS B:295binding site for residue ZN B 1001
07AC7SOFTWARECYS B:284 , CYS B:287 , CYS B:313 , CYS B:316binding site for residue ZN B 1002
08AC8SOFTWARECYS B:319 , CYS B:322 , HIS B:342 , CYS B:345binding site for residue ZN B 1003
09AC9SOFTWARECYS B:334 , CYS B:337 , CYS B:360 , CYS B:363binding site for residue ZN B 1004
10AD1SOFTWAREPHE B:333 , ASP B:335 , HOH B:1139 , HOH B:1141 , HOH B:1147 , HOH B:1150binding site for residue NA B 1007
11AD2SOFTWAREASP A:263 , PHE A:264 , SER A:290 , CYS A:313 , ILE A:314 , GLY C:12 , ALA C:15binding site for Di-peptide GLY C 13 and ALY C 14
12AD3SOFTWAREASP A:263 , PHE A:264 , LEU A:266 , ARG A:289 , SER A:290 , CYS A:313 , ILE A:314 , GLY C:13 , PRO C:16binding site for Di-peptide ALY C 14 and ALA C 15

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I3L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:347 -Pro A:348
2Asn B:347 -Pro B:348

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I3L)

(-) Exons   (0, 0)

(no "Exon" information available for 5I3L)

(-) 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    
   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:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................ee......ee.......hhhhhhhhh.......................eee......eee.................hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5i3l A 256 VIPNNYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECKSCILCGTSENDDQLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELL 367
                                   265       275       285       295       305       315       325       335       345       355       365  


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........................ee......ee.......hhhhhhhhh...................hhh.eee......eee.................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5i3l B 255 TVIPNNYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECKSCILCGTSENDDQLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLK 368
                                   264       274       284       294       304       314       324       334       344       354       364    


Chain C from PDB  Type:PROTEIN  Length:17
                                                 
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author .eehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 5i3l C   1 ARTKQTARKSTGGxAPR  17
                                    10   |   
                                        14-ALY
   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 5I3L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I3L)

(-) Gene Ontology  (19, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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    Asn A:347 - Pro A:348   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPF3_HUMAN | Q92784: 2kwj 2kwk 2kwn 2kwo
        H3C_HUMAN | Q6NXT2: 3kv4 4z5t 5bwn 5bwo 5f6k

(-) Related Entries Specified in the PDB File

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