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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 3-AMINO-4-METHYL-1,3-DIHYDRO-2H-INDOL-2-ONE (N10042A)
 
Authors :  R. Nowak, T. Krojer, C. Johansson, N. Pearce, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, N. A. Burgess-Brown, C. H. Arrowsm C. Bountra, A. M. Edwards, F. Von Delft, P. E. Brennan, U. Oppermann
Date :  09 Mar 16  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
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 N10042A
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, UNP 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, LYSINE-SPECIFIC DEMETHYLASE 5B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 22)

Asymmetric/Biological Unit (7, 22)
No.NameCountTypeFull Name
1BY41Ligand/Ion(3R)-3-AZANYL-4-METHYL-1,3-DIHYDROINDOL-2-ONE
2CL1Ligand/IonCHLORIDE ION
3DMS3Ligand/IonDIMETHYL SULFOXIDE
4EDO13Ligand/Ion1,2-ETHANEDIOL
5MN2Ligand/IonMANGANESE (II) ION
6PO41Ligand/IonPHOSPHATE ION
7ZN1Ligand/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 A1755
02AC2SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , HOH A:2114 , HOH A:2115 , HOH A:2122BINDING SITE FOR RESIDUE MN A1756
03AC3SOFTWAREHIS A:399BINDING SITE FOR RESIDUE MN A1757
04AC4SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2157 , HOH A:2235BINDING SITE FOR RESIDUE PO4 A1758
05AC5SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , EDO A:1762 , HOH A:2169BINDING SITE FOR RESIDUE EDO A1759
06AC6SOFTWAREPHE A:83 , GLY A:426 , ALA A:427 , ASP A:428 , PHE A:434 , LEU A:487 , VAL A:489 , HOH A:2086BINDING SITE FOR RESIDUE EDO A1760
07AC7SOFTWAREARG A:666 , TYR A:734 , THR A:737BINDING SITE FOR RESIDUE EDO A1761
08AC8SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , EDO A:1759 , HOH A:2160BINDING SITE FOR RESIDUE EDO A1762
09AC9SOFTWAREPRO A:30 , VAL A:568BINDING SITE FOR RESIDUE EDO A1763
10BC1SOFTWAREASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , VAL A:693 , GLY A:711 , LEU A:713BINDING SITE FOR RESIDUE EDO A1764
11BC2SOFTWAREGLY A:524 , ARG A:584 , HOH A:2239BINDING SITE FOR RESIDUE EDO A1765
12BC3SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2082 , HOH A:2186BINDING SITE FOR RESIDUE EDO A1766
13BC4SOFTWAREHIS A:564 , GLU A:565BINDING SITE FOR RESIDUE EDO A1767
14BC5SOFTWAREARG A:98 , CYS A:497 , HIS A:499 , EDO A:1769 , BY4 A:1774 , HOH A:2048 , HOH A:2049BINDING SITE FOR RESIDUE EDO A1768
15BC6SOFTWAREGLN A:88 , GLN A:96 , THR A:97 , TYR A:425 , SER A:495 , PHE A:496 , CYS A:497 , EDO A:1768BINDING SITE FOR RESIDUE EDO A1769
16BC7SOFTWARELEU A:101 , GLY A:481 , ASP A:502 , ASN A:601 , DMS A:1771 , HOH A:2047 , HOH A:2123BINDING SITE FOR RESIDUE EDO A1770
17BC8SOFTWARETRP A:486 , TYR A:488 , ALA A:599 , VAL A:600 , ASN A:601 , EDO A:1770BINDING SITE FOR RESIDUE DMS A1771
18BC9SOFTWAREGLU A:631 , LYS A:635 , GLU A:683 , PHE A:700 , ARG A:735 , TYR A:736BINDING SITE FOR RESIDUE DMS A1772
19CC1SOFTWARETRP A:504 , GLU A:531 , HIS A:617 , LEU A:621 , HOH A:2120 , HOH A:2139 , HOH A:2241BINDING SITE FOR RESIDUE DMS A1773
20CC2SOFTWARETYR A:425 , TYR A:488 , PHE A:496 , ASN A:509 , LYS A:517 , EDO A:1768 , HOH A:2085BINDING SITE FOR RESIDUE BY4 A1774
21CC3SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419BINDING SITE FOR RESIDUE CL A1775

(-) 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 5FYU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FYU)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee......eehhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eeeeeeee.................hhhhhhhhh.............hhhhhh...hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh...........eeeee........hhhhhhhh...hhh.eeeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fyu A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAES 754
                             ||     33        43        53        63        73        83        93       376       386       396       406       416       426       436      |447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       
                             0|                                                                        101|                                                                 443|                                                                                                                                                                                                                                                                                                                     
                             26                                                                         375                                                                  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 5FYU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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(-) 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 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

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
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
5fyz CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10063A
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
5fze CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3960
5fzf CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3962
5fzg CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3948
5fzh 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)
5fzi CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC3095
5fzk CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT N,3-DIMETHYL-N -(PYRIDIN-3-YLMETHYL)-1,2-OXAZOLE-5-CARBOXAMIDE ( N10051A) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzl CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 3-METHYL-N- PYRIDIN-4-YL-1,2-OXAZOLE-5-CARBOXAMIDE (N09954A) ( LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
5fzm CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT 5-(2-FLUOROPHENYL )-1,3-OXAZOLE-4-CARBOXYLIC ACID (N09989B) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04 -1 FRAGMENT SCREENING)