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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CANCER GENOMIC DNA MUTATOR APOBEC3B
 
Authors :  K. Shi, K. Kurahashi, H. Aihara
Date :  21 Jul 15  (Deposition) - 07 Oct 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A
Keywords :  Apobec, Deaminase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shi, M. A. Carpenter, K. Kurahashi, R. S. Harris, H. Aihara
Crystal Structure Of The Dna Deaminase Apobec3B Catalytic Domain.
J. Biol. Chem. V. 290 28120 2015
PubMed-ID: 26416889  |  Reference-DOI: 10.1074/JBC.M115.679951

(-) Compounds

Molecule 1 - DNA DC-DU-EDITING ENZYME APOBEC-3B
    Chains: A
    EC Number: 3.5.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 187-378
    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

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:253 , CYS A:284 , CYS A:289 , HOH A:551binding site for residue ZN A 401
2AC2SOFTWAREARG A:211 , ARG A:212 , GLN A:213 , THR A:214 , ASN A:240 , HIS A:253 , TYR A:313 , HOH A:532 , HOH A:551 , HOH A:558binding site for residue GOL A 402
3AC3SOFTWAREARG A:212 , GLN A:213 , ASN A:240 , SER A:250 , GLY A:251 , GLU A:342 , HOH A:507 , HOH A:558binding site for residue GOL A 403
4AC4SOFTWAREARG A:252 , GLU A:292 , ARG A:311 , ASP A:314 , TYR A:315 , HOH A:505 , HOH A:509binding site for residue GOL A 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CQI)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...........eeeeeeeeee..eeee.hhhheeee.....hhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cqi A 190 RYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQL 379
                                   199       209       219       229       239 ||    257       267       277       287       297       307       317       327       337       347       357       367       377  
                                                                             241|                                                                                                                                 
                                                                              250
   Legend:   → Mismatch (orange background)
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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 5CQI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5cqd 5cqh 5cqk