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(-) Description

Title :  ALKBH2 F102A CROSS-LINKED TO UNDAMAGED DSDNA
 
Authors :  B. Chen, J. Gan, C. G. Yang
Date :  28 Aug 13  (Deposition) - 26 Feb 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Enzyme Function Initiative, Center For Eukaryotic Structural Genomics, Cesg, Rossmann Fold, Oxidoreductase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Chen, J. Gan, C. G. Yang
The Complex Structures Of Alkbh2 Mutants Cross-Linked To Dsdna Reveal The Conformational Swing Of β -Hairpin
Sci China Chem V. 57 307 2014
PubMed: search  |  Reference-DOI: 10.1007/S11426-013-5029-Z

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2
    Chains: A
    EC Number: 1.14.11.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ALKBH2, ABH2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 2, DNA OXIDATIVE DEMETHYLASE ALKBH2, OXY DC1
 
Molecule 2 - DNA-1
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC SOURCE
    Synthetic: YES
 
Molecule 3 - DNA-2
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC SOURCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
12YR1Mod. Nucleotide2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:171 , ASP A:173 , HIS A:236 , HOH A:422 , HOH A:423 , HOH A:424BINDING SITE FOR RESIDUE MG A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MG2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:228 -Pro A:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MG2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MG2)

(-) Exons   (0, 0)

(no "Exon" information available for 4MG2)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...eeeee..eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......eeee..........eeeeeee..eeeeeee.....eeeeee...eeeee..hhhhheeeee.........eeeeeee..... Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------eeee--eeee----eeeee-----eee--eee------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mg2 A  55 MSWRHIRAEGLDSSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVAGKWHSVPRKQATYGDAGLTYTFSGLTLSPKPWIPVLERIRDHVSGVTGQTFNFVLINRYKDGSDHICEHRDDERELASPIASVSFGASRDFVFRHKDSVAVVRLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILLM 259
                                    64        74        84        94       104       114       124       134       144       154       164       174    || 186       196     ||214       224       234       244       254     
                                                                                                                                                      179|                 202|                                                
                                                                                                                                                       182                  211                                                


Chain B from PDB  Type:DNA  Length:14
                                              
                 4mg2 B  10 TCGACAGTGAGACA  23
                                    19    


Chain C from PDB  Type:DNA  Length:13
                                             
                 4mg2 C  28 TGTCTCAxTGTCG  40
                                   |37   
                                  35-2YR
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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 4MG2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MG2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MG2)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  4mg2
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  ALKB2_HUMAN | Q6NS38
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  1.14.11.33
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALKB2_HUMAN | Q6NS38: 3btx 3bty 3btz 3bu0 3buc 3h8o 3h8r 3h8x 3rzg 3rzh 3rzj 3rzk 3rzl 3rzm 3s57 3s5a 4mgt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MG2)