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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 :  1.88
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  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3PGE2Ligand/IonTRIETHYLENE GLYCOL
4ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:253 , CYS A:284 , CYS A:289 , HOH A:510binding 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:504 , HOH A:505 , HOH A:510binding site for residue GOL A 402
3AC3SOFTWARETYR A:215 , PHE A:237 , CYS A:239 , THR A:337 , TYR A:338 , ASP A:339 , HOH A:503 , HOH A:556 , HOH A:558 , HOH A:562 , HOH A:570binding site for residue GOL A 403
4AC4SOFTWAREARG A:252 , LEU A:259 , ASP A:260 , ASP A:314 , TYR A:315 , PGE A:405 , NA A:406binding site for residue PGE A 404
5AC5SOFTWAREPRO A:206 , ARG A:252 , LEU A:259 , ASP A:260 , GLU A:292 , ASP A:314 , TYR A:315 , PGE A:404 , NA A:406binding site for residue PGE A 405
6AC6SOFTWAREASP A:260 , ASP A:314 , PGE A:404 , PGE A:405binding site for residue NA A 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CQK)

(-) 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
(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:181
                                                                                                                                                                                                                     
               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
                 5cqk A 190 RYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQ 378
                                   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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  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 5CQK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5cqi 5td5 5tkm

(-) Related Entries Specified in the PDB File

5cqd 5cqh 5cqk