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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 :  2.08
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
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, C
    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

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:253 , CYS A:284 , CYS A:289 , GOL A:502 , HOH A:603binding site for residue ZN A 501
2AC2SOFTWAREARG A:211 , ARG A:212 , GLN A:213 , THR A:214 , ASN A:240 , HIS A:253 , TRP A:281 , TYR A:313 , ZN A:501 , HOH A:601 , HOH A:603binding site for residue GOL A 502
3AC3SOFTWARESER A:286binding site for residue GOL A 503
4AC4SOFTWARECYS A:239 , GLU A:241 , ARG A:257 , HOH A:612 , HOH A:631binding site for residue GOL A 504
5AC5SOFTWAREGLU A:342 , ASP A:346binding site for residue GOL A 505
6AC6SOFTWAREHIS C:253 , CYS C:284 , CYS C:289 , HOH C:602binding site for residue ZN C 501
7AC7SOFTWAREARG C:211 , ARG C:212 , GLN C:213 , THR C:214 , ASN C:240 , HIS C:253 , TYR C:313 , HOH C:602binding site for residue GOL C 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CQD)

(-) Sequences/Alignments

Asymmetric 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:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh...........eeeeeeeeee..eeee.....eeee.....hhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cqd A 186 MEILRYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQ 378
                                   195       205       215       225       235     ||253       263       273       283       293       303       313       323       333       343       353       363       373     
                                                                                 241|                                                                                                                                
                                                                                  250                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh...........eeeeeeeeee..eeeeeeeeeeeee.....hhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhhhhhh..eeeeeeeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cqd C 188 ILRYLMDPDTFTSNFNNDPLVLRRRQTYLCYEVERLDNGTSVKMDQHMGFLCNESGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIKAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQL 379
                                   197       207       217       227       237   ||  255       265       275       285       295       305       315       325       335       345       355       365       375    
                                                                               241|                                                                                                                                 
                                                                                250
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5CQD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5cqh 5cqi 5cqk