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(-) Description

Title :  STRUCTURE OF HUMAN ALKBH5 CRYSTALLIZED IN THE PRESENCE OF CITRATE
 
Authors :  W. Tempel, X. Chao, K. Liu, A. Dong, T. Cerovina, H. He, C. Bountra, C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genomics Consor (Sgc)
Date :  20 Dec 13  (Deposition) - 26 Feb 14  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dioxygenase, Rna Demethylase, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Xu, K. Liu, W. Tempel, M. Demetriades, W. Aik, C. J. Schofield, J. Min
Structures Of Human Alkbh5 Demethylase Reveal A Unique Binding Mode For Specific Single-Stranded N6-Methyladenosin Rna Demethylation.
J. Biol. Chem. V. 289 17299 2014
PubMed-ID: 24778178  |  Reference-DOI: 10.1074/JBC.M114.550350

(-) Compounds

Molecule 1 - RNA DEMETHYLASE ALKBH5
    ChainsA, B
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid511693
    FragmentUNP RESIDUES 74-294
    GeneALKBH5, ABH5, OFOXD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 5, ALPHA- KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 5

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 36)

Asymmetric Unit (4, 36)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2GOL2Ligand/IonGLYCEROL
3UNL2Ligand/IonUNKNOWN LIGAND
4UNX30Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL
3UNL1Ligand/IonUNKNOWN LIGAND
4UNX15Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (4, 18)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL
3UNL1Ligand/IonUNKNOWN LIGAND
4UNX15Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:263 , THR A:265 , HOH A:411 , HOH A:487BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWARELYS A:132 , ASN A:193 , ILE A:201 , HIS A:204 , ASP A:206 , ILE A:215 , SER A:217 , HIS A:266 , ILE A:281 , ARG A:283 , HOH A:416BINDING SITE FOR RESIDUE CIT A 302
3AC3SOFTWAREALA B:114 , GLY B:117 , LEU B:118 , TYR B:119 , VAL B:124 , ARG B:126 , HOH B:404 , HOH B:486BINDING SITE FOR RESIDUE GOL B 301
4AC4SOFTWARELYS B:132 , ASN B:193 , ILE B:201 , HIS B:204 , ASP B:206 , ILE B:215 , SER B:217 , HIS B:266 , ILE B:281 , ARG B:283 , HOH B:406BINDING SITE FOR RESIDUE CIT B 302

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:230 -A:267
2B:230 -B:267

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:213 -Pro A:214
2Arg B:213 -Pro B:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O61)

(-) Exons   (0, 0)

(no "Exon" information available for 4O61)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhh...hhh.eeee..eeeeee......................hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee.hhhhh.........eeeee...eeeeehhhhhhh..eeehhhhh...eeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o61 A  76 LQKEEEARKVKSGIRQMRLFSQDECAKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTYGPGQERLYPPGDVDEIPEWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRLET 294
                                    85        95       105       115       125       135     ||152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
                                                                                           141|                                                                                                                                                 
                                                                                            149                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhh...hhh.eeee..eeeeee.....................hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee.hhhhh.........eeeee...eeeeehhhhhhh..eeehhhhh...eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o61 B  77 QKEEEARKVKSGIRQMRLFSQDECAKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTGPGQERLYPPGDVDEIPEWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRLE 293
                                    86        96       106       116       126       136   ||  154       164       174       184       194       204       214       224       234       244       254       264       274       284         
                                                                                         140|                                                                                                                                                
                                                                                          149                                                                                                                                                

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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 4O61)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O61)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O61)

(-) Gene Ontology  (16, 16)

Asymmetric 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 | Q6P6C24nj4 4nrm 4nro 4nrp 4nrq 4o7x 4oct

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4O61)