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(-) Description

Title :  JMJD5 IN COMPLEX WITH 2-OXOGLUTARATE
 
Authors :  P. A. Del Rizzo, R. C. Trievel
Date :  10 Aug 12  (Deposition) - 05 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Jmjc, Beta Barrel, Fe(Ii) And 2-Oxoglutarate Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. A. Del Rizzo, S. Krishnan, R. C. Trievel
Crystal Structure And Functional Analysis Of Jmjd5 Indicate An Alternate Specificity And Function.
Mol. Cell. Biol. V. 32 4044 2012
PubMed-ID: 22851697  |  Reference-DOI: 10.1128/MCB.00513-12

(-) Compounds

Molecule 1 - JMJC DOMAIN-CONTAINING PROTEIN 5
    ChainsA
    EC Number1.14.11.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDR146
    Expression System StrainBL21(ROSETTA2)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentJMJC DOMAIN (UNP RESIDUES 183-416)
    GeneJMJD5, JMJD5 (AMINO ACIDS 183 - 416), KDM8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJMJC DOMAIN-CONTAINING PROTEIN 5, JUMONJI DOMAIN-CONTAINING PROTEIN 5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3CO1Ligand/IonCOBALT (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:321 , ASP A:323 , HIS A:400 , AKG A:502 , HOH A:601BINDING SITE FOR RESIDUE CO A 501
2AC2SOFTWARETYR A:272 , TRP A:310 , SER A:318 , HIS A:321 , ASP A:323 , ASN A:327 , LYS A:336 , HIS A:400 , VAL A:402 , SER A:412 , TRP A:414 , CO A:501 , HOH A:601 , HOH A:604BINDING SITE FOR RESIDUE AKG A 502
3AC3SOFTWAREGLN A:227 , GLU A:228 , ILE A:229 , GLY A:231 , CYS A:232 , LEU A:370 , HOH A:719BINDING SITE FOR RESIDUE BME A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GJZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GJZ)

(-) 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee..hhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh..eeeeee..eeeeeehhhhhhhhh.......eeeeeehhhhhhhhhhh....hhhhhhh..hhhhheeeeeee....eeeee....eeeeeeee..eeeeeehhhhhhhh.......................hhhhhhh..eeeee....eeee....eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gjz A 182 STVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS 416
                                   191       201       211       221       231       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408        
                                                                                    240|                                                                                                                                                                        
                                                                                     248                                                                                                                                                                        

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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 4GJZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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
        KDM8_HUMAN | Q8N3713uyj 4aap 4gaz 4gjy 4qu1 5fbj

(-) Related Entries Specified in the PDB File

4gjy