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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH S40563A
 
Authors :  V. Srikannathasan, Y. V. Le Bihan, A. Szykowska, C. Johansson, C. Gile C. H. Arrowsmith, A. M. Edwards, C. Bountra, F. Von Delft, U. Opperman
Date :  15 Sep 16  (Deposition) - 28 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Lysine-Specific Demethylase 5B, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Srikannathasan
Crystal Structure Of Human Jarid1B In Complex With S40563A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5B,LYSINE-SPECIFIC DEMETHYLASE 5B
    Chains: A
    EC Number: 1.14.11.-, 1.14.11.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-LIC-BSE
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: KDM5B, JARID1B, PLU1, RBBP2H1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CCT365714
    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,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  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
15UJ1Ligand/Ion8-[4-[2-[4-[3,5-BIS(CHLORANYL)PHENYL]PIPERIDIN-1-YL]ETHYL]PYRAZOL-1-YL]-3~{H}-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MN2Ligand/IonMANGANESE (II) ION
5ZN1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718binding site for residue ZN A 801
2AC2SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419binding site for residue MN A 802
3AC3SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:914binding site for residue EDO A 803
4AC4SOFTWAREGLY A:524 , ARG A:584binding site for residue EDO A 804
5AC5SOFTWARETRP A:504 , GLU A:531 , ARG A:584 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623binding site for residue DMS A 805
6AC6SOFTWARETRP A:486 , TYR A:488 , GLU A:501 , SER A:507 , ALA A:599 , VAL A:600 , ASN A:601 , 5UJ A:808binding site for residue DMS A 806
7AC7SOFTWAREARG A:98 , CYS A:497 , HIS A:499 , 5UJ A:808 , HOH A:959binding site for residue DMS A 807
8AC8SOFTWARETYR A:425 , ASP A:428 , GLY A:481 , TRP A:486 , TYR A:488 , PHE A:496 , HIS A:499 , GLU A:501 , ASN A:509 , LYS A:517 , TRP A:519 , HIS A:587 , DMS A:806 , DMS A:807 , MN A:809 , HOH A:902 , HOH A:956binding site for residue 5UJ A 808
9AC9SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , 5UJ A:808 , HOH A:956binding site for residue MN A 809

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:708 -A:725

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LW9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LW9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LW9)

(-) Exons   (0, 0)

(no "Exon" information available for 5LW9)

(-) 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:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee......eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeehhhhh...........hhhhhhh........hhhhh..................eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh........ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh..........eeeee...........hhhhh...hhh.eeeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lw9 A  25 MFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAES 754
                                    34        44        54        64        74        84        94     ||377       387       397       407       417       427       437     ||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      
                                                                                                     100|                                                                  443|                                                                                                                                                                                                                                                                                                                     
                                                                                                      374                                                                   445
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5LW9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LW9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LW9)

(-) Gene Ontology  (34, 34)

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
        KDM5B_HUMAN | Q9UGL1: 2ma5 2mny 2mnz 5a1f 5a3n 5a3p 5a3t 5a3w 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 5lwb

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