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(-) Description

Title :  LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N3 (4'-[(2-PHENYLETHYL)CARBAMOYL][2,2'-BIPYRIDINE]-4-CARBOXYLIC ACID)
 
Authors :  J. R. Horton, X. Cheng
Date :  20 Mar 16  (Deposition) - 27 Jul 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A
Keywords :  Demethylase Inhibition, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Horton, X. Liu, M. Gale, L. Wu, J. R. Shanks, X. Zhang, P. J. Webber, J. S. Bell, S. C. Kales, B. T. Mott, G. Rai, D. J. Jansen, M. J. Henderson, D. J. Urban, M. D. Hall, A. Simeonov, D. J. Maloney, M. A. Johns, H. Fu, A. Jadhav, P. M. Vertino, Q. Yan, X. Cheng
Structural Basis For Kdm5A Histone Lysine Demethylase Inhibition By Diverse Compounds.
Cell Chem Biol V. 23 769 2016
PubMed-ID: 27427228  |  Reference-DOI: 10.1016/J.CHEMBIOL.2016.06.006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5A
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VariantGOLD C-PLUS
    FragmentLINKED KDM5A JMJ DOMAIN, UNP RESIDUES 1-87 AND 348-588
    GeneKDM5A, JARID1A, RBBP2, RBP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
16E71Ligand/Ion4'-[(2-PHENYLETHYL)CARBAMOYL][2,2'-BIPYRIDINE]-4-CARBOXYLIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:73 , TYR A:409 , TYR A:472 , SER A:479 , PHE A:480 , HIS A:483 , GLU A:485 , LYS A:501 , TRP A:503 , HIS A:571 , MN A:602 , HOH A:815binding site for residue 6E7 A 601
2AC2SOFTWAREHIS A:483 , GLU A:485 , HIS A:571 , 6E7 A:601 , HOH A:815binding site for residue MN A 602
3AC3SOFTWARELYS A:45 , ARG A:73 , HIS A:509 , HOH A:803binding site for residue EDO A 603
4AC4SOFTWAREGLU A:64 , VAL A:65 , LYS A:66 , ARG A:429binding site for residue EDO A 604
5AC5SOFTWARESER A:399 , ILE A:539 , MET A:540 , ASN A:541 , HOH A:778 , HOH A:806binding site for residue EDO A 605
6AC6SOFTWAREMET A:380 , PRO A:381 , GLU A:485 , ASP A:486 , HIS A:487 , TRP A:488 , HOH A:703 , HOH A:718 , HOH A:898binding site for residue GOL A 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5IVC)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee........hhhhhhhhhhhhhh...eeee.................ee..eeee.....................eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeehhhhh............hhhhhhhhhh..hhhhh.....hhhhhhh...eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivc A  12 EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT 588
                                    21        31        41        51        61        71        81 ||    354       364       374       384       394       404       414       424       434       444       454     ||470       480       490       500       510       520       530       540       550       560       570       580        
                                                                                                  83|                                                                                                              460|                                                                                                                         
                                                                                                  347                                                                                                               467                                                                                                                         

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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 5IVC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

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
        KDM5A_HUMAN | P293752jxj 2kgg 2kgi 3gl6 5c11 5ceh 5e6h 5isl 5ivb 5ive 5ivf 5ivj 5ivv 5ivy 5iw0 5iwf 5k4l 5v9p 5v9t

(-) Related Entries Specified in the PDB File

5isl 5ivb 5ive 5ivf 5ivj 5ivv 5ivy 5iw0 5iwf