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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALKBH5
 
Authors :  W. S. Aik, M. A. Mcdonough, C. J. Schofield
Date :  08 Nov 13  (Deposition) - 15 Jan 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Double-Stranded Beta Helix, Jelly-Roll Motif, Dioxygenase, Rna Demethylase, Rna, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Aik, J. S. Scotti, H. Choi, L. Gong, M. Demetriades, C. J. Schofield, M. A. Mcdonough
Structure Of Human Rna N6-Methyladenine Demethylase Alkbh5 Provides Insights Into Its Mechanisms Of Nucleic Acid Recognition And Demethylation.
Nucleic Acids Res. V. 42 4741 2014
PubMed-ID: 24489119  |  Reference-DOI: 10.1093/NAR/GKU085

(-) Compounds

Molecule 1 - RNA DEMETHYLASE ALKBH5
    ChainsA, B
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentALKBH5 RESIDUES 66-292
    GeneABH5, ALKBH5, 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, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MN2Ligand/IonMANGANESE (II) ION
3NO33Ligand/IonNITRATE ION
4UN92Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
3NO31Ligand/IonNITRATE ION
4UN91Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
3NO32Ligand/IonNITRATE ION
4UN91Ligand/IonN-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:204 , ASP A:206 , HIS A:266 , HOH A:405 , HOH A:416 , HOH A:439BINDING SITE FOR RESIDUE MN A 301
02AC2SOFTWARESER A:217 , ILE A:268 , ARG A:277 , HOH A:478 , HOH A:542BINDING SITE FOR RESIDUE NO3 A 302
03AC3SOFTWAREGLU A:212 , ARG A:286 , LEU A:287 , ASP A:288BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWAREILE A:201 , VAL A:202 , HIS A:204 , UN9 A:305 , HOH A:532BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREARG A:130 , CYS A:200 , ILE A:201 , VAL A:202 , GLN A:233 , GOL A:304 , CYS B:200 , UN9 B:305BINDING SITE FOR RESIDUE UN9 A 305
06AC6SOFTWAREHIS B:204 , ASP B:206 , HIS B:266 , HOH B:422 , HOH B:431 , HOH B:434BINDING SITE FOR RESIDUE MN B 301
07AC7SOFTWARESER B:217 , ILE B:268 , ARG B:277 , HOH B:479BINDING SITE FOR RESIDUE NO3 B 302
08AC8SOFTWAREGLN A:271 , HOH A:428 , LYS B:235 , PRO B:236 , ILE B:237BINDING SITE FOR RESIDUE NO3 B 303
09AC9SOFTWAREARG A:93 , GLU B:166 , GLU B:184BINDING SITE FOR RESIDUE GOL B 304
10BC1SOFTWARECYS A:200 , UN9 A:305 , ARG B:130 , CYS B:200 , ILE B:201 , VAL B:202 , GLN B:233 , HOH B:480BINDING SITE FOR RESIDUE UN9 B 305

(-) 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 4NJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4NJ4)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhh...hhh.eeee..eeeeee...eee......eee.........hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee.hhhhhh........eeeee...eeeeehhhhhhh..eeehhhhh...eeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nj4 A  69 SDYEEQQLQKEEEARKVKSGIRQMRLFSQDECAKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTYGAQPGQERLYPPGDVDEIPEWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRL 292
                                    78        88        98       108       118       128       138     ||153       163       173       183       193       203       213       223       233       243       253       263       273       283         
                                                                                                     144|                                                                                                                                              
                                                                                                      150                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhheeeee..hhhhhhhhhhhhhhhhhhhhh...hhh.eee...eeeeee...ee....ee.........hhhhhhhhhhhhhhh.........eeeeeee.....eeee..........eeeeee...eeeee.hhhhh.........eeeee...eeeeehhhhhhh..eeehhhhh...eeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nj4 B  78 KEEEARKVKSGIRQMRLFSQDECAKIEARIDEVVSRAEKGLYNEHTVDRAPLRNKYFFGEGYTYGQERLYPPGDVDEIPEWVHQLVIQKLVEHRVIPEGFVNSAVINDYQPGGCIVSHVDPIHIFERPIVSVSFFSDSALCFGCKFQFKPIRVSEPVLSLPVRRGSVTVLSGYAADEITHCIRPQDIKERRAVIILRKTRLDAPRL 292
                                    87        97       107       117       127       137    || 156       166       176       186       196       206       216       226       236       246       256       266       276       286      
                                                                                          142|                                                                                                                                            
                                                                                           152                                                                                                                                            

   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 4NJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NJ4)

(-) 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 | Q6P6C24nrm 4nro 4nrp 4nrq 4o61 4o7x 4oct

(-) Related Entries Specified in the PDB File

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