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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 2-(2-OXO-2,3-DIHYDRO-1H-INDOL-3-YL)ACETONITRILE (N10063A)
 
Authors :  R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-D A. Szykowska, N. A. Burgess-Brown, C. H. Arrowsmith, C. Bountra, A. M. F. Von Delft, P. E. Brennan, U. Oppermann
Date :  10 Mar 16  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Jarid1B, Plu1, Pandda, Fragment Soaking, X-Ray Fragment Screening, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, F. Von Delft, N. A. Burgess-Brown C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Crystal Structure Of The Catalytic Domain Of Human Jarid1B In Complex With N10063A
To Be Published
PubMed: search

(-) 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 26-101,374-770
    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, 21)

Asymmetric/Biological Unit (7, 21)
No.NameCountTypeFull Name
1DMS3Ligand/IonDIMETHYL SULFOXIDE
2EDO12Ligand/Ion1,2-ETHANEDIOL
3MN1Ligand/IonMANGANESE (II) ION
4NA1Ligand/IonSODIUM ION
5NYK1Ligand/Ion[(3S)-2-OXO-2,3-DIHYDRO-1H-INDOL-3-YL]ACETONITRILE
6PO41Ligand/IonPHOSPHATE ION
7ZN2Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
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
03AC3SOFTWARETYR A:488 , PHE A:496 , HIS A:499 , LYS A:517 , HIS A:587 , MN A:1757 , DMS A:1770 , HOH A:2180 , HOH A:2187 , HOH A:2193 , HOH A:2203BINDING SITE FOR RESIDUE NYK A1756
04AC4SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , NYK A:1756 , HOH A:2180 , HOH A:2187BINDING SITE FOR RESIDUE MN A1757
05AC5SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2245 , HOH A:2250BINDING SITE FOR RESIDUE PO4 A1758
06AC6SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2262BINDING SITE FOR RESIDUE EDO A1759
07AC7SOFTWAREPHE A:83 , GLY A:426 , ALA A:427 , LEU A:487 , TYR A:488 , VAL A:489 , HOH A:2128BINDING SITE FOR RESIDUE EDO A1760
08AC8SOFTWAREARG A:666 , THR A:737 , HOH A:2340BINDING SITE FOR RESIDUE EDO A1761
09AC9SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , LEU A:665 , HOH A:2239BINDING SITE FOR RESIDUE EDO A1762
10BC1SOFTWAREPRO A:30 , VAL A:568BINDING SITE FOR RESIDUE EDO A1763
11BC2SOFTWAREASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , VAL A:693 , GLY A:711 , LEU A:712 , LEU A:713 , HOH A:2342BINDING SITE FOR RESIDUE EDO A1764
12BC3SOFTWAREGLY A:524 , ARG A:584 , HOH A:2206 , HOH A:2343BINDING SITE FOR RESIDUE EDO A1765
13BC4SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2121 , HOH A:2281BINDING SITE FOR RESIDUE EDO A1766
14BC5SOFTWAREHIS A:564 , GLU A:565BINDING SITE FOR RESIDUE EDO A1767
15BC6SOFTWARELYS A:80 , LYS A:720 , CYS A:723 , HOH A:2325BINDING SITE FOR RESIDUE EDO A1768
16BC7SOFTWARECYS A:634 , LYS A:635 , GLU A:683 , ARG A:735 , TYR A:736BINDING SITE FOR RESIDUE EDO A1769
17BC8SOFTWAREGLN A:88 , GLN A:96 , THR A:97 , TYR A:425 , SER A:495 , PHE A:496 , CYS A:497 , NYK A:1756BINDING SITE FOR RESIDUE DMS A1770
18BC9SOFTWARETRP A:486 , TYR A:488 , SER A:507 , VAL A:600 , ASN A:601 , HOH A:2193BINDING SITE FOR RESIDUE DMS A1771
19CC1SOFTWAREILE A:500 , TRP A:504 , HIS A:617 , LEU A:621 , ARG A:623 , HOH A:2186BINDING SITE FOR RESIDUE DMS A1772
20CC2SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2062 , HOH A:2064BINDING SITE FOR RESIDUE NA A1773
21CC3SOFTWAREHOH A:2344BINDING SITE FOR RESIDUE EDO A1774

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FYZ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee.....eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeee................hhhhhhhh...............hhhhh...hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh...........eeeee...........hhhhh...hhh.eeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fyz A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93       377       387       397       407       417       427       437    || 449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749    
                             0|                                                                        101|                                                               442|                                                                                                                                                                                                                                                                                                                    
                             26                                                                         376                                                                445
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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 5FYZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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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 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

5fxv CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N05859B
5fxw CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH FUMARATE
5fxx CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH OXALOACETATE
5fxz CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH CITRATE
5fy0 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH L-MALATE
5fy1 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N08619B
5fy4 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH SUCCINATE
5fy5 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH FUMARATE
5fy7 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH SUCCINATE
5fy8 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH D- THREO-ISOCITRATE
5fy9 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH PYRUVATE
5fyb CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC1648
5fyc CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE
5fyh CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE
5fyi CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE
5fym CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fys CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fyt CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N09996A
5fyu CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10042A
5fyv CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH OXALOACETATE
5fyy CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N05798A
5fz0 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N11213A
5fz1 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH E48115B
5fz3 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N08776B
5fz4 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10057A
5fz6 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT N05859B ( LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fz7 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT ETHYL 2- AMINO-4-THIOPHEN-2-YLTHIOPHENE-3-CARBOXYLATE (N06131B ) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fz8 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MALATE
5fz9 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT THIENO(3,2 -B)THIOPHENE-5-CARBOXYLIC ACID (N06263B) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04 -1 FRAGMENT SCREENING)
5fza CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 2-PIPERIDIN-4- YLOXY-5-(TRIFLUOROMETHYL)PYRIDINE (N10072A) (LIGAND MODELLED BASED ON PANDDA EVENT MAP)
5fzb CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT 4- PYRIDYLTHIOUREA (N06275B) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzc CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MAYBRIDGE FRAGMENT 4,5- DIHYDRONAPHTHO(1,2-B)THIOPHENE-2-CARBOXYLICACID (N11181A ) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzd CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH L-2-HYDROXYGLUTARATE