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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH 3D FRAGMENT (3R)-1-[(3-PHENYL-1,2,4-OXADIAZOL-5-YL)METHYL]PYRROLIDIN-3-OL (N10057A) (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING)
 
Authors :  R. Nowak, T. Krojer, N. Pearce, R. Talon, P. Collins, C. Johansson, C. Gi K. Kupinska, C. Strain-Damerell, A. Szykowska, N. A. Burgess-Brown, C. H. Arrowsmith, C. Bountra, A. M. Edwards, F. Von Delft, P. E. Brenna U. Oppermann
Date :  10 Mar 16  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Jarid1B, Plu1, Fragment Screening, Structural Genomics Consortium, Sgc, Diamond I04-1, Pandda (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, R. Talon, P. Collins, N. A. Burgess-Brown, C. H. Arrowsmith, C. Bountra, A. M. Edwards, F. Von Delft, P. E. Brennan, U. Oppermann
Crystal Structure Of The Catalytic Domain Of Human Jarid1B In Complex With N10057A
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, 19)

Asymmetric/Biological Unit (7, 19)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3EDO10Ligand/Ion1,2-ETHANEDIOL
4MN1Ligand/IonMANGANESE (II) ION
5P6B1Ligand/Ion(3S)-1-[(3-PHENYL-1,2,4-OXADIAZOL-5-YL)METHYL]PYRROLIDIN-3-OL
6PO41Ligand/IonPHOSPHATE ION
7ZN2Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
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
03AC3SOFTWAREGLU A:662 , LYS A:663 , ARG A:666 , ARG A:670 , TYR A:736 , THR A:737 , LEU A:738 , LEU A:741 , EDO A:1761 , HOH A:2203 , HOH A:2204BINDING SITE FOR RESIDUE P6B A1756
04AC4SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , HOH A:2103 , HOH A:2104 , HOH A:2109BINDING SITE FOR RESIDUE MN A1757
05AC5SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2040BINDING SITE FOR RESIDUE CL A1758
06AC6SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , EDO A:1762 , HOH A:2154BINDING SITE FOR RESIDUE EDO A1759
07AC7SOFTWAREPHE A:83 , GLY A:426 , ALA A:427 , ASP A:428 , PHE A:434 , LEU A:487 , VAL A:489BINDING SITE FOR RESIDUE EDO A1760
08AC8SOFTWAREARG A:666 , TYR A:734 , P6B A:1756 , HOH A:2204BINDING SITE FOR RESIDUE EDO A1761
09AC9SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , LEU A:665 , EDO A:1759BINDING 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:713BINDING SITE FOR RESIDUE EDO A1764
12BC3SOFTWAREGLY A:524 , TYR A:525 , ARG A:584 , HOH A:2205BINDING SITE FOR RESIDUE EDO A1765
13BC4SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2077 , HOH A:2169BINDING SITE FOR RESIDUE EDO A1766
14BC5SOFTWARELYS A:536 , HIS A:564BINDING SITE FOR RESIDUE EDO A1767
15BC6SOFTWAREGLN A:88 , GLN A:96 , TYR A:425 , SER A:495 , PHE A:496 , CYS A:497BINDING SITE FOR RESIDUE EDO A1768
16BC7SOFTWARETYR A:488 , PHE A:496 , ASN A:509 , LYS A:517 , HOH A:2118BINDING SITE FOR RESIDUE DMS A1769
17BC8SOFTWARETRP A:486 , TYR A:488 , VAL A:600 , ASN A:601BINDING SITE FOR RESIDUE DMS A1770
18BC9SOFTWAREILE A:500 , TRP A:504 , GLU A:531 , ARG A:584 , HIS A:617 , TYR A:618 , LEU A:621 , HOH A:2108BINDING SITE FOR RESIDUE DMS A1771
19CC1SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2140 , HOH A:2144BINDING SITE FOR RESIDUE PO4 A1772

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FZ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FZ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 5FZ4)

(-) 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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   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:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee....eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeee................hhhhhhhhh.....................hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh........ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh...........eeeee........hhhhhhhh...hhh.eeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fz4 A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITAICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93      |378       388       398       408       418       428       438   ||  450       460       470      |481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751  
                             0|                                                                       100|                                                               442|                             477|                                                                                                                                                                                                                                                                                  
                             26                                                                        376                                                                445                              479
   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 5FZ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FZ4)

(-) 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 5fyz 5fz0 5fz1 5fz3 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
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
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)