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(-) Description

Title :  CRYSTAL STRUCTURE OF DOUBLE TUDOR DOMAIN OF HUMAN LYSINE DEMETHYLASE KDM4A
 
Authors :  F. Wang, Z. Su, J. M. Denu, G. N. Phillips Jr. , Enzyme Discovery For N Product Biosynthesis (Natpro)
Date :  13 Aug 15  (Deposition) - 25 Nov 15  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Double Tudor Domain, Reader Domain, Structural Genomics, Psi-2, Protein Structure Initiative, Enzyme Discovery For Natural Product Biosynthesis, Natpro, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Su, F. Wang, J. H. Lee, K. E. Stephens, R. Papazyan, E. Voronina, K. A. Krautkramer, A. Raman, J. J. Thorpe, M. D. Boersma, V. I. Kuznetsov, M. D. Miller, S. D. Taverna, G. N. Phillips, J. M. Denu
Reader Domain Specificity And Lysine Demethylase-4 Family Function.
Nat Commun V. 7 13387 2016
PubMed-ID: 27841353  |  Reference-DOI: 10.1038/NCOMMS13387

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4A
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JUMONJI DOMAIN-CONTAINING PROTEIN 2A

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:910 , SER A:994 , GLN A:995 , HOH A:1234 , HOH A:1261 , HOH A:1269binding site for residue SO4 A 1101
2AC2SOFTWAREARG A:921 , ARG A:966 , GLN A:987binding site for residue SO4 A 1102
3AC3SOFTWARELYS B:910 , SER B:994 , GLN B:995 , HOH B:1219 , HOH B:1261 , HOH B:1279binding site for residue SO4 B 1101
4AC4SOFTWAREARG B:921 , ARG B:966 , GLN B:987binding site for residue SO4 B 1102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D6X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D6X)

 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) 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:115
                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeehhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                5d6x A  897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
                                   906       916       926       936       946       956       966       976       986       996      1006     


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeeeeeeeeeeeeeee....eeeeehhhhh...hhhhhh......eeeee.....eeeeeeeeeeeeeeeeeee....eeeehhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                5d6x B  897 QSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP 1011
                                   906       916       926       936       946       956       966       976       986       996      1006
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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 5D6X)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (25, 25)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM4A_HUMAN | O75164: 2gf7 2gfa 2gp3 2gp5 2oq6 2oq7 2os2 2ot7 2ox0 2p5b 2pxj 2q8c 2q8d 2q8e 2qqr 2qqs 2vd7 2wwj 2ybk 2ybp 2ybs 3njy 3pdq 3rvh 3u4s 4ai9 4bis 4gd4 4ura 4v2v 4v2w 5a7n 5a7o 5a7p 5a7q 5a7s 5a7w 5a80 5anq 5d6w 5d6y 5f2s 5f2w 5f32 5f37 5f39 5f3c 5f3e 5f3g 5f3i 5f5i 5fpv 5fwe 5fy8 5fyc 5fyh 5fyi 5ly1 5ly2 5tvr 5tvs

(-) Related Entries Specified in the PDB File

5d6w 5d6y