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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALKBH5 IN COMPLEX WITH ALPHA-KETOGLUTARATE
 
Authors :  C. Feng, Z. Chen, Y. Liu
Date :  27 Nov 13  (Deposition) - 19 Mar 14  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Alkbh5, 6-Methyl Adenosine, Protein/Dna Interaction, Human Dioxygenase, Metal-Binding, Nucleus, Demethylation, Rna Repair, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Feng, Y. Liu, G. Wang, Z. Deng, Q. Zhang, W. Wu, Y. Tong, C. Cheng, Z. Chen
Crystal Structures Of The Human Rna Demethylase Alkbh5 Reveal Basis For Substrate Recognition
J. Biol. Chem. V. 289 11571 2014
PubMed-ID: 24616105  |  Reference-DOI: 10.1074/JBC.M113.546168

(-) Compounds

Molecule 1 - RNA DEMETHYLASE ALKBH5
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 66-292
    Gene: ABH5, ALKBH5, OFOXD1
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 5, ALPHA- KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:204 , ASP A:206 , HIS A:266 , AKG A:302 , HOH A:401BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREASN A:193 , TYR A:195 , ILE A:201 , HIS A:204 , ASP A:206 , HIS A:266 , ILE A:268 , ARG A:277 , VAL A:279 , ILE A:281 , MN A:301 , HOH A:445BINDING SITE FOR RESIDUE AKG A 302

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:230 -A:267

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:213 -Pro A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NRO)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhh.......eee...eeeeee......................hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeee....eeeee.hhhhh.........eeeee...eeeeehhhhhhh..eeehhhhh...eeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nro A  73 EQQLQKEEEARKVKSGIRQMRLFSQDECAKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTYGPGQERLYPPGDVDEIPEWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRL 292
                                    82        92       102       112       122       132       142|      159       169       179       189       199       209       219       229       239       249       259       269       279       289   
                                                                                               142|                                                                                                                                              
                                                                                                150
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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 4NRO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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
        ALKB5_HUMAN | Q6P6C2: 4nj4 4nrm 4nrp 4nrq 4o61 4o7x 4oct

(-) Related Entries Specified in the PDB File

4nrm 4nrp 4nrq