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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH PYRIDINE-2,6-DICARBOXYLIC ACID (PDCA)
 
Authors :  V. Srikannathasan, C. Johansson, C. Gileadi, J. Kopec, C. Strain-Dame K. Kupinska, N. A. Burgess-Brown, F. Von Delft, C. H. Arrowsmith, C. B A. M. Edwards, U. Oppermann
Date :  03 Jun 15  (Deposition) - 17 Jun 15  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Lysine-Specific Demethylase 5B (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Johansson, S. Velupillai, A. Tumber, A. Szykowska, E. S. Hookway, R. P. Nowak, C. Strain-Damerell, C. Gileadi, M. Philpott, N. Burgess-Brown, N. Wu, J. Kopec, A. Nuzzi, H. Steuber, U. Egner, V. Badock, S. Munro, N. B. Lathangue, S. Westaway, J. Brown, N. Athanasou, R. Prinjha, P. E. Brennan, U. Oppermann
Structural Analysis Of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Nat. Chem. Biol. V. 12 539 2016
PubMed-ID: 27214403  |  Reference-DOI: 10.1038/NCHEMBIO.2087

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5B
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-LIC-BSE
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: JMJC DOMAIN, RESIDUES 26-101,374-772
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric/Biological Unit (7, 10)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MN1Ligand/IonMANGANESE (II) ION
4NA1Ligand/IonSODIUM ION
5PD21Ligand/IonPYRIDINE-2,4-DICARBOXYLIC ACID
6PO41Ligand/IonPHOSPHATE ION
7ZN2Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A1754
02AC2SOFTWARECYS A:706 , CYS A:708 , CYS A:723 , CYS A:725BINDING SITE FOR RESIDUE ZN A1755
03AC3SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2049BINDING SITE FOR RESIDUE NA A1756
04AC4SOFTWAREARG A:98 , TYR A:425 , TYR A:488 , PHE A:496 , HIS A:499 , GLU A:501 , LYS A:517 , TRP A:519 , HIS A:587 , MN A:1758 , HOH A:2098 , HOH A:2108 , HOH A:2109 , HOH A:2113 , HOH A:2228BINDING SITE FOR RESIDUE PD2 A1757
05AC5SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , PD2 A:1757 , HOH A:2109BINDING SITE FOR RESIDUE MN A1758
06AC6SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2150BINDING SITE FOR RESIDUE PO4 A1759
07AC7SOFTWAREILE A:500 , TRP A:504 , GLU A:531 , MET A:534 , LEU A:541 , PHE A:542 , LEU A:552 , VAL A:553 , TYR A:586 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2102 , HOH A:2107 , HOH A:2129 , HOH A:2155 , HOH A:2229BINDING SITE FOR RESIDUE EPE A1760
08AC8SOFTWAREASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , VAL A:693 , GLY A:711 , LEU A:712 , LEU A:713BINDING SITE FOR RESIDUE EDO A1761
09AC9SOFTWAREVAL A:674 , ILE A:675 , LEU A:732 , HOH A:2186 , HOH A:2190BINDING SITE FOR RESIDUE EDO A1762
10BC1SOFTWAREALA A:386 , ASP A:387 , LYS A:390 , MET A:491 , CYS A:492 , GLU A:515 , GLY A:593 , PHE A:594BINDING SITE FOR RESIDUE EDO A1763

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A3W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A3W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A3W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A3W)

(-) Exons   (0, 0)

(no "Exon" information available for 5A3W)

(-) 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:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee......eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeee................hhhhhhh.......hhhhhh..hhhhhh...hhhhh..eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh...........eeeee...........hhhhh...hhh.eeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a3w A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93      |376       386       396       406       416       426       436     ||448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748     
                             0|                                                                       100|                                                                 442|                                                                                                                                                                                                                                                                                                                    
                             26                                                                        374                                                                  445
   Legend:   → Mismatch (orange background)
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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 5A3W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A3W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A3W)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a3w
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  KDM5B_HUMAN | Q9UGL1
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  1.14.11.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM5B_HUMAN | Q9UGL1: 2ma5 2mny 2mnz 5a1f 5a3n 5a3p 5a3t 5fpl 5fpu 5fun 5fup 5fv3 5fy4 5fy5 5fy9 5fyb 5fys 5fyt 5fyu 5fyv 5fyy 5fyz 5fz0 5fz1 5fz3 5fz4 5fz6 5fz7 5fz8 5fz9 5fza 5fzb 5fzc 5fzd 5fze 5fzf 5fzg 5fzh 5fzi 5fzk 5fzl 5fzm 5lw9 5lwb

(-) Related Entries Specified in the PDB File

5a3n CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDOAM25A
5a3t CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)( ETHYL)AMINO)-2-OXOETHYL)AMINO)METHYL) ISONICOTINIC ACID ).