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(-) Description

Title :  THE STRUCTURE OF JMJD7 WITH ALPHA-KG
 
Authors :  H. L. Liu, C. Wang, G. Y. Zhang
Date :  10 Jul 14  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Jmj-C Domain, Demethylation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Liu, C. Wang, C. Dege, F. K. Ning, J. Weisz, K. Hansen, Z. Z. Chen, C. H. Pan, C. W. Nho, J. Nix, P. Marrack, J. Kappler, J. Hagmen, G. Y. Zhan
The Structure Of Jmjd7 With Alpha-Kg
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - JMJC DOMAIN-CONTAINING PROTEIN 7
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: JMJD7
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: JUMONJI DOMAIN-CONTAINING PROTEIN 7, JMJD7

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:178 , ASP A:180 , HIS A:277 , AKG A:502BINDING SITE FOR RESIDUE NI A 501
2AC2SOFTWARETYR A:127 , TRP A:167 , THR A:175 , HIS A:178 , ASN A:184 , TYR A:186 , LYS A:193 , HIS A:277 , VAL A:279 , TRP A:291 , NI A:501 , HOH A:612BINDING SITE FOR RESIDUE AKG A 502
3AC3SOFTWAREGLN B:131 , HIS B:178 , ASP B:180 , HIS B:277 , AKG B:502BINDING SITE FOR RESIDUE NI B 501
4AC4SOFTWARETYR B:127 , TRP B:167 , THR B:175 , HIS B:178 , ASP B:180 , ASN B:184 , TYR B:186 , LYS B:193 , HIS B:277 , VAL B:279 , ASN B:289 , NI B:501 , HOH B:611 , HOH B:624BINDING SITE FOR RESIDUE AKG B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QU2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QU2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QU2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QU2)

(-) Exons   (0, 0)

(no "Exon" information available for 4QU2)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh......ee....hhhhhhhhh......eeee......hhhhhhhhhhhhhhhh..eeeeeee......eee..eeee.eeeeeehhhhhhhhhh......eeee....hhhhhhhhhhhhhh...hhhhhhhhh....eeeeeee.....eeee...eeeeeeeee..eeeeeehhhhhhhh..eeeeeeeeee.....eeeee......eee............hhhhhhh..eeeee...eeeee....eeeeee...eeeeeeeee...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qu2 A  -1 GSMAEAALEAVRRALQEFPAAARDLNVPRVVPYLDEPPSPLCFYRDWVCPNRPCIIRNALQHWPALQKWSLSYLRATVGSTEVSVAVTPDGYADAVRGDRFVMPAERRLPISHVLDVLEGRAQHPGVLYVQKQCSNLPTELPQLLSDIESHVPWASESLGKMPDAVNFWLGDASAVTSLHKDHYENLYCVVSGEKHFLLHPPSDRPFIPYNLYTPATYQLTEEGTFRVVDEEAMEKVPWIPLDPLAPDLTQYPSYSQAQALHCTVRAGEMLYLPALWFHHVQQSHGCIAVNFWYDMEYDLKYSYFQLMDTLTRATGLD 316
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        


Chain B from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.....ee....hhhhhhhhh......eee......hhhhhh.hhhhhhhhhh..eeeeeee......eee..eeee.eeeeeehhhhhhhhhh......eeee....hhhhhhhhhhhhhh...hhhhhhhhh....eeeeeee.....eeee...eeeeeeeee..eeeeeehhhhhhhh..eeeeeeeeee.....eeeee......eee............hhhhhhh..eeeee....eeee....eeeeee...eeeeeeeee...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qu2 B  -1 GSMAEAALEAVRRALQEFPAAARDLNVPRVVPYLDEPPSPLCFYRDWVCPNRPCIIRNALQHWPALQKWSLSYLRATVGSTEVSVAVTPDGYADAVRGDRFVMPAERRLPISHVLDVLEGRAQHPGVLYVQKQCSNLPTELPQLLSDIESHVPWASESLGKMPDAVNFWLGDASAVTSLHKDHYENLYCVVSGEKHFLLHPPSDRPFIPYNLYTPATYQLTEEGTFRVVDEEAMEKVPWIPLDPLAPDLTQYPSYSQAQALHCTVRAGEMLYLPALWFHHVQQSHGCIAVNFWYDMEYDLKYSYFQLMDTLTRATGLD 316
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308
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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 4QU2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QU2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QU2)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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  JMJD7_MOUSE | P0C872
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 Related Entries

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

UniProtKB/Swiss-Prot
        JMJD7_MOUSE | P0C872: 4qsz

(-) Related Entries Specified in the PDB File

4qsz 4qu1