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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) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
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
    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, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DC1Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
3EDO4Ligand/Ion1,2-ETHANEDIOL
4ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:253 , CYS A:284 , CYS A:289 , EDO A:405binding site for residue ZN A 401
2AC2SOFTWAREARG A:252 , ASP A:260 , ASP A:314 , TYR A:319 , LYS A:320 , ARG A:372 , HOH A:504 , HOH A:549 , HOH A:554 , HOH A:559 , HOH A:598 , HOH A:616 , HOH A:620binding site for residue DC A 402
3AC3SOFTWAREILE A:335 , SER A:370 , ARG A:374binding site for residue CL A 403
4AC4SOFTWAREPRO A:206 , ARG A:252 , TRP A:287 , GLU A:292 , HOH A:510 , HOH A:580binding site for residue EDO A 404
5AC5SOFTWARETHR A:214 , HIS A:253 , GLU A:255 , SER A:282 , CYS A:284 , CYS A:289 , ZN A:401binding site for residue EDO A 405
6AC6SOFTWARECYS A:239 , THR A:337 , TYR A:338 , ASP A:339 , HOH A:560 , HOH A:562binding site for residue EDO A 406
7AC7SOFTWAREASP A:339 , GLU A:340 , TYR A:343 , HOH A:516 , HOH A:622 , HOH A:640binding site for residue EDO A 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CQH)

(-) 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:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...........eeeeeeeeee..eeee.hhhheeee.....hhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cqh A 189 LRYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQL 379
                                   198       208       218       228       238  ||   256       266       276       286       296       306       316       326       336       346       356       366       376   
                                                                              241|                                                                                                                                 
                                                                               250
   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 5CQH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5cqd 5cqi 5cqk