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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN APOBEC3B N-TERMINAL DOMAIN
 
Authors :  X. Xiao, H. Yang, V. Arutiunian, G. Besse, C. Morimoto, B. Zirkle, X. S. C
Date :  07 Oct 16  (Deposition) - 14 Jun 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Deaminase, Apobec (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xiao, H. Yang, V. Arutiunian, Y. Fang, G. Besse, C. Morimoto, B. Zirkle, X. S. Chen
Structural Determinants Of Apobec3B Non-Catalytic Domain Fo Molecular Assembly And Catalytic Regulation.
Nucleic Acids Res. 2017
PubMed-ID: 28575276  |  Reference-DOI: 10.1093/NAR/GKX362

(-) Compounds

Molecule 1 - DNA DC->DU-EDITING ENZYME APOBEC-3B
    Chains: A, B
    EC Number: 3.5.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Taxid: 83333
    Gene: APOBEC3B
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: A3B,PHORBOLIN-1-RELATED PROTEIN,PHORBOLIN-2/3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , CYS A:97 , CYS A:100 , HOH A:526binding site for residue ZN A 401
2AC2SOFTWAREHIS B:66 , CYS B:97 , CYS B:100 , HOH B:524binding site for residue ZN B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:80 -Pro A:81
2Leu B:80 -Pro B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TKM)

(-) 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
(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:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhhhh.........eeeeeeeeeeee..eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhh......eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhee..........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkm A   7 NPMERMDRDTFYDNFENEPILSGRSYTWLCYEVKIKRGRSNLLWDTGVFRGQVYFKPQYHAEMCFLSWFCGNQLPADKCFQITWFVSWTPCPDCVAKLAEFLSEHPNVTLTISAARLYYYSERDYRRALCRLSQAGARVKIMDYEEFAYCWENFVDNEGQQFMPWYKFDENYAFLHRTLKEILR 190
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhhhh.........eeeeeeeeeeee..eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhh......eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhee..........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkm B   7 NPMERMDRDTFYDNFENEPILSGRSYTWLCYEVKIKRGRSNLLWDTGVFRGQVYFKPQYHAEMCFLSWFCGNQLPADKCFQITWFVSWTPCPDCVAKLAEFLSEHPNVTLTISAARLYYYSERDYRRALCRLSQAGARVKIMDYEEFAYCWENFVDNEGQQFMPWYKFDENYAFLHRTLKEILR 190
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
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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 5TKM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  3.5.4.-
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 Related Entries

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UniProtKB/Swiss-Prot
        ABC3B_HUMAN | Q9UH17: 2nbq 5cqd 5cqh 5cqi 5cqk 5td5

(-) Related Entries Specified in the PDB File

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