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(-) Description

Title :  LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N19 [2-(5-((4-CHLORO-2-METHYLBENZYL)OXY)-1H-PYRAZOL-1-YL)ISONICOTINIC ACID]
 
Authors :  J. R. Horton, X. Cheng
Date :  21 Mar 16  (Deposition) - 27 Jul 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
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
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD C-PLUS
    Fragment: LINKED KDM5A JMJ DOMAIN, UNP RESIDUES 1-87 AND 348-588
    Gene: KDM5A, JARID1A, RBBP2, RBP2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ISTONE 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  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
16EP1Ligand/Ion2-{5-[(4-CHLORO-2-METHYLPHENYL)METHOXY]-1H-PYRAZOL-1-YL}PYRIDINE-4-CARBOXYLIC ACID
2AKG1Ligand/Ion2-OXOGLUTARIC ACID
3EDO2Ligand/Ion1,2-ETHANEDIOL
4GOL2Ligand/IonGLYCEROL
5MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:73 , GLN A:75 , TYR A:409 , ALA A:411 , ASP A:412 , TYR A:472 , PHE A:480 , HIS A:483 , GLU A:485 , LYS A:501 , TRP A:503 , HIS A:571 , AKG A:602 , MN A:603 , HOH A:776binding site for residue 6EP A 601
2AC2SOFTWARELYS A:45 , SER A:479 , PHE A:480 , CYS A:481 , HIS A:483 , GLN A:535 , LEU A:536 , 6EP A:601 , HOH A:701binding site for residue AKG A 602
3AC3SOFTWAREHIS A:483 , GLU A:485 , HIS A:571 , 6EP A:601 , HOH A:776binding site for residue MN A 603
4AC4SOFTWAREGLU A:64 , VAL A:65 , LYS A:66 , ARG A:429binding site for residue EDO A 604
5AC5SOFTWAREILE A:539 , MET A:540 , ASN A:541 , HOH A:710 , HOH A:765binding site for residue EDO A 605
6AC6SOFTWARESER A:375 , ASN A:379 , MET A:380 , PRO A:381 , ASP A:486 , HIS A:487 , HOH A:715 , HOH A:802binding site for residue GOL A 606
7AC7SOFTWARELYS A:45 , GLN A:75 , ARG A:76 , LEU A:77 , GLU A:79 , SER A:479 , HOH A:701 , HOH A:745 , HOH A:848binding site for residue GOL A 607

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IW0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IW0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IW0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IW0)

(-) Exons   (0, 0)

(no "Exon" information available for 5IW0)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee....hhhhhhhhhhhhhhhhhh...eeee.................ee..eeee...................eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeeeeeeehhhhh............hhhhhhhhhh..hhhhh.....hhhhhhh...eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iw0 A  12 EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT 588
                                    21        31        41        51        61        71        81 ||    356       366       376       386       396       406       416       426       436       446       456   ||  472       482       492       502       512       522       532       542       552       562       572       582      
                                                                                                  83|                                                                                                            460|                                                                                                                         
                                                                                                  349                                                                                                             467
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5IW0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IW0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IW0)

(-) 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 | P29375: 2jxj 2kgg 2kgi 3gl6 5c11 5ceh 5e6h 5isl 5ivb 5ivc 5ive 5ivf 5ivj 5ivv 5ivy 5iwf 5k4l 5v9p 5v9t

(-) Related Entries Specified in the PDB File

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