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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC1648
 
Authors :  R. Nowak, V. Srikannathasan, D. Rotili, C. Johansson, C. Gileadi, K. Ku C. Strain-Damerell, A. Szykowska, F. Von Delft, N. A. Burgess-Brown C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Date :  05 Mar 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Jarid1B, Plu1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nowak, V. Srikannathasan, D. Rotili, 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 Mc1648
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5B, 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 AND 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, LYSINE-SPECIFIC DEMETHYLASE 5B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 28)

Asymmetric/Biological Unit (5, 28)
No.NameCountTypeFull Name
177J2Ligand/IonN-HYDROXY-3-[(6-OXO-4-PHENYL-1,6-DIHYDROPYRIMIDIN-2-YL)SULFANYL]PROPANAMIDE
2DMS4Ligand/IonDIMETHYL SULFOXIDE
3EDO16Ligand/Ion1,2-ETHANEDIOL
4MN4Ligand/IonMANGANESE (II) ION
5ZN2Ligand/IonZINC ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A 1754
02AC2SOFTWARECYS A:706 , CYS A:708 , CYS A:723 , CYS A:725BINDING SITE FOR RESIDUE ZN A 1755
03AC3SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , 77J A:1761 , HOH A:2241BINDING SITE FOR RESIDUE MN A 1756
04AC4SOFTWAREHOH A:2432BINDING SITE FOR RESIDUE MN A 1757
05AC5SOFTWAREHIS A:399BINDING SITE FOR RESIDUE MN A 1758
06AC6SOFTWARESER A:544BINDING SITE FOR RESIDUE MN A 1759
07AC7SOFTWAREGLU A:31 , CYS A:32 , PRO A:33 , VAL A:34 , ILE A:55 , HOH A:2014BINDING SITE FOR RESIDUE 77J A 1760
08AC8SOFTWARETYR A:488 , PHE A:496 , HIS A:499 , GLU A:501 , SER A:507 , ASN A:509 , LYS A:517 , TRP A:519 , HIS A:587 , ASN A:591 , MN A:1756 , EDO A:1770 , DMS A:1780 , DMS A:1781 , HOH A:2233 , HOH A:2241BINDING SITE FOR RESIDUE 77J A 1761
09AC9SOFTWAREPHE A:83 , GLY A:426 , ALA A:427 , LEU A:487 , VAL A:489 , HOH A:2176BINDING SITE FOR RESIDUE EDO A 1762
10BC1SOFTWAREARG A:666 , LEU A:732 , TYR A:734 , THR A:737 , HOH A:2377 , HOH A:2460BINDING SITE FOR RESIDUE EDO A 1763
11BC2SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , EDO A:1776 , HOH A:2327BINDING SITE FOR RESIDUE EDO A 1764
12BC3SOFTWAREPRO A:30 , VAL A:568 , TYR A:569BINDING SITE FOR RESIDUE EDO A 1765
13BC4SOFTWAREASP 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 A 1766
14BC5SOFTWAREGLY A:524 , TYR A:525 , ARG A:584 , LEU A:610 , HOH A:2270 , HOH A:2463 , HOH A:2464BINDING SITE FOR RESIDUE EDO A 1767
15BC6SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2169 , HOH A:2376BINDING SITE FOR RESIDUE EDO A 1768
16BC7SOFTWAREHIS A:564BINDING SITE FOR RESIDUE EDO A 1769
17BC8SOFTWAREVAL A:99 , TRP A:486 , TYR A:488 , 77J A:1761 , DMS A:1781 , HOH A:2119 , HOH A:2224BINDING SITE FOR RESIDUE EDO A 1770
18BC9SOFTWAREASP A:387 , ALA A:388 , VAL A:398 , HOH A:2129 , HOH A:2137 , HOH A:2465BINDING SITE FOR RESIDUE EDO A 1771
19CC1SOFTWARELEU A:405 , LYS A:408 , GLU A:409 , ASP A:676 , HOH A:2005BINDING SITE FOR RESIDUE EDO A 1772
20CC2SOFTWAREGLU A:678 , LYS A:731 , ARG A:733 , HOH A:2438BINDING SITE FOR RESIDUE EDO A 1773
21CC3SOFTWAREMET A:680 , HOH A:2408 , HOH A:2466BINDING SITE FOR RESIDUE EDO A 1774
22CC4SOFTWAREPRO A:28 , PRO A:29 , PRO A:30 , MET A:562 , LEU A:750 , HOH A:2452BINDING SITE FOR RESIDUE EDO A 1775
23CC5SOFTWAREVAL A:615 , ARG A:619 , THR A:697 , EDO A:1764 , HOH A:2325 , HOH A:2430BINDING SITE FOR RESIDUE EDO A 1776
24CC6SOFTWARELYS A:80 , GLU A:721 , CYS A:723 , SER A:724 , HOH A:2434BINDING SITE FOR RESIDUE EDO A 1777
25CC7SOFTWAREGLU A:631 , GLU A:683 , TYR A:736BINDING SITE FOR RESIDUE DMS A 1778
26CC8SOFTWAREILE A:500 , TRP A:504 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2245 , HOH A:2280 , HOH A:2340BINDING SITE FOR RESIDUE DMS A 1779
27CC9SOFTWAREGLN A:88 , GLN A:96 , THR A:97 , TYR A:425 , SER A:495 , PHE A:496 , CYS A:497 , 77J A:1761 , HOH A:2237BINDING SITE FOR RESIDUE DMS A 1780
28DC1SOFTWARETRP A:486 , TYR A:488 , GLU A:501 , SER A:507 , ASN A:601 , 77J A:1761 , EDO A:1770BINDING SITE FOR RESIDUE DMS A 1781

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FYB)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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......hhhhhhhhhhhhhhh.....eeeeeeee................hhhhhhhh.......hhhhh...hhhhh...hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh........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
                 5fyb A  24 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 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     
                                                                                                       101|                                                                442|                                                                                                                                                                                                                                                                                                                    
                                                                                                        375                                                                 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 5FYB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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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 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

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
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
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)