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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH L-2-HYDROXYGLUTARATE
 
Authors :  R. Nowak, J. Kopec, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Da A. Szykowska, F. Von Delft, N. A. Burgess-Brown, C. H. Arrowsmith, C. A. M. Edwards, U. Oppermann
Date :  14 Mar 16  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Jarid1B, Plu1, Tca Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Nowak, J. Kopec, 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 L-2-Hydroxyglutarate
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, 20)

Asymmetric/Biological Unit (7, 20)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO13Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MN1Ligand/IonMANGANESE (II) ION
5PO41Ligand/IonPHOSPHATE ION
6S2G1Ligand/Ion(2S)-2-HYDROXYPENTANEDIOIC ACID
7ZN2Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:706 , CYS A:708 , CYS A:723 , CYS A:725BINDING SITE FOR RESIDUE ZN A 1754
02AC2SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A 1755
03AC3SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , S2G A:1771 , HOH A:2136BINDING SITE FOR RESIDUE MN A 1756
04AC4SOFTWARETRP A:504 , GLU A:531 , LEU A:541 , PHE A:542 , LEU A:552 , ARG A:584 , TYR A:586 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2134 , HOH A:2140 , HOH A:2265BINDING SITE FOR RESIDUE EPE A 1757
05AC5SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2193BINDING SITE FOR RESIDUE EDO A 1758
06AC6SOFTWAREGLY A:426 , ALA A:427 , ASP A:428 , PHE A:434 , LEU A:487 , VAL A:489BINDING SITE FOR RESIDUE EDO A 1759
07AC7SOFTWAREARG A:666 , LEU A:732 , TYR A:734 , THR A:737 , HOH A:2259 , HOH A:2267BINDING SITE FOR RESIDUE EDO A 1760
08AC8SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , LEU A:665BINDING SITE FOR RESIDUE EDO A 1761
09AC9SOFTWAREPRO A:30 , PRO A:567 , VAL A:568BINDING SITE FOR RESIDUE EDO A 1762
10BC1SOFTWAREASP 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 1763
11BC2SOFTWAREGLY A:524 , TYR A:525 , LEU A:610 , HOH A:2154 , HOH A:2269BINDING SITE FOR RESIDUE EDO A 1764
12BC3SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2104 , HOH A:2211BINDING SITE FOR RESIDUE EDO A 1765
13BC4SOFTWAREHIS A:564BINDING SITE FOR RESIDUE EDO A 1766
14BC5SOFTWARETRP A:486 , TYR A:488 , GLU A:501 , ALA A:599 , ASN A:601BINDING SITE FOR RESIDUE EDO A 1767
15BC6SOFTWARETYR A:425 , GLY A:426 , TYR A:488 , VAL A:489 , GLY A:490 , SER A:494 , SER A:495 , ASN A:591 , S2G A:1771 , HOH A:2150BINDING SITE FOR RESIDUE EDO A 1768
16BC7SOFTWAREGLU A:631 , CYS A:634 , LYS A:635 , TYR A:736 , HOH A:2124BINDING SITE FOR RESIDUE EDO A 1769
17BC8SOFTWAREHIS A:50BINDING SITE FOR RESIDUE EDO A 1770
18BC9SOFTWARETYR 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 , ALA A:599 , MN A:1756 , EDO A:1768 , HOH A:2136 , HOH A:2150 , HOH A:2272BINDING SITE FOR RESIDUE S2G A 1771
19CC1SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2055BINDING SITE FOR RESIDUE CL A 1772
20CC2SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2181 , HOH A:2185BINDING SITE FOR RESIDUE PO4 A 1773

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FZD)

(-) 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:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee.....eee...eehhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....eeeeeeee................hhhhhhh........................hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.eee..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
                 5fzd A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93     ||379       389       399       409       419       429       439  ||   451       461       471       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|                                                                       99|                                                               442|                                                                                                                                                                                                                                                                                                                    
                             26                                                                       376                                                                445
   Legend:   → Mismatch (orange background)
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    → 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 5FZD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5fzd
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  KDM5B_HUMAN | Q9UGL1
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  1.14.11.-
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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 5fze 5fzf 5fzg 5fzh 5fzi 5fzk 5fzl 5fzm 5lw9 5lwb

(-) Related Entries Specified in the PDB File

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)
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)
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)
5fzo CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JMJD1C