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(-) Description

Title :  COMPLEX STRUCTURE OF JMJD5 AND SUBSTRATE
 
Authors :  H. L. Liu, Y. Wang, C. Wang, G. Y. Zhang
Date :  14 Dec 15  (Deposition) - 14 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Liu, Y. Wang, C. Wang, S. D. Dai, G. Y. Zhang
To Be Published
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 8
    Chains: A
    EC Number: 1.14.11.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KDM8, JMJD5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC 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
2NMM1Ligand/Ion(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOICACID
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR 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 , NMM A:502 , ZN A:503 , HOH A:648binding site for residue AKG A 501
2AC2SOFTWAREGLU A:238 , TYR A:243 , TYR A:272 , GLN A:275 , TRP A:310 , SER A:318 , HIS A:321 , ASP A:323 , TRP A:414 , AKG A:501 , ZN A:503 , HOH A:632 , HOH A:633binding site for residue NMM A 502
3AC3SOFTWAREHIS A:321 , ASP A:323 , HIS A:400 , AKG A:501 , NMM A:502binding site for residue ZN A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FBJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FBJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FBJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FBJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5FBJ)

(-) 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eee..hhhhhhhhh......eeee......hhhhhhhhhhhhhhhh..eeeeee.........eeeeeehhhhhhhhh.......eeeeeehhhhhhhhhhh....hhhhhhh..hhhhheeeeeee....eeeee....eeeeeeee..eeeeeehhhhhhhhh......................hhhhh....eeeee....eeee....eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fbj A 181 GSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS 416
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410
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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 5FBJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FBJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FBJ)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  5fbj
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  KDM8_HUMAN | Q8N371
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM8_HUMAN | Q8N371: 3uyj 4aap 4gaz 4gjy 4gjz 4qu1

(-) Related Entries Specified in the PDB File

4qu1 CRYSTAL STRUCTURE OF HUMAN JMJD5 JMJ-C DOMAIN