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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH GSKJ1
 
Authors :  V. Srikannathasan, R. Nowak, C. Johansson, C. Gileadi, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann
Date :  03 Dec 15  (Deposition) - 13 Jan 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription, Lysine-Specific Demethylase 5B (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Johansson, S. Velupillai, A. Tumber, A. Szykowska, E. S. Hookway, R. P. Nowak, C. Strain-Damerell, C. Gileadi, M. Philpott, N. Burgess-Brown, N. Wu, J. Kopec, A. Nuzzi, H. Steuber, U. Egner, V. Badock, S. Munro, N. B. Lathangue, S. Westaway, J. Brown, N. Athanasou, R. Prinjha, P. E. Brennan, U. Oppermann
Structural Analysis Of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Nat. Chem. Biol. V. 12 539 2016
PubMed-ID: 27214403  |  Reference-DOI: 10.1038/NCHEMBIO.2087

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 5B
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PFB-LIC-BSE
    Expression System Strain: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: JMJC DOMAIN, RESIDUES 26-772
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3K0I1Ligand/Ion3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC ACID
4MN2Ligand/IonMANGANESE (II) ION
5PO42Ligand/IonPHOSPHATE ION
6ZN2Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
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
03AC3SOFTWAREGLN A:88 , GLN A:96 , THR A:97 , ARG A:98 , TYR A:425 , TYR A:488 , SER A:495 , PHE A:496 , HIS A:499 , GLU A:501 , ASN A:509 , LYS A:517 , MN A:1758 , HOH A:2117 , HOH A:2123 , HOH A:2132BINDING SITE FOR RESIDUE K0I A1756
04AC4SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2045BINDING SITE FOR RESIDUE MN A1757
05AC5SOFTWAREHIS A:499 , GLU A:501 , K0I A:1756 , HOH A:2117 , HOH A:2123BINDING SITE FOR RESIDUE MN A1758
06AC6SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2172 , HOH A:2176BINDING SITE FOR RESIDUE PO4 A1759
07AC7SOFTWARETRP A:486 , TYR A:488 , GLU A:501 , ALA A:599 , VAL A:600 , ASN A:601 , HOH A:2123BINDING SITE FOR RESIDUE PO4 A1760
08AC8SOFTWAREILE A:500 , TRP A:504 , GLU A:531 , PHE A:542 , GLN A:551 , ARG A:584 , TYR A:586 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2121 , HOH A:2153BINDING SITE FOR RESIDUE EPE A1761
09AC9SOFTWAREILE A:475 , ALA A:477 , PHE A:627 , SER A:628 , GLU A:631 , MET A:632 , HOH A:2222BINDING SITE FOR RESIDUE EDO A1762
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 A1763
11BC2SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2201 , HOH A:2206BINDING SITE FOR RESIDUE EDO A1764
12BC3SOFTWAREALA A:386 , ASP A:387 , LYS A:390 , VAL A:398 , MET A:491 , CYS A:492 , GLU A:515 , GLY A:593 , PHE A:594BINDING SITE FOR RESIDUE EDO A1765
13BC4SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2184BINDING SITE FOR RESIDUE EDO A1766

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FPU)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   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:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee.....eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......eeeeeeee.................hhhhhh.........hhhhh...........hhhhh..eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.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
                 5fpu A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93      |377       387       397       407       417       427       437     ||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     
                             0|                                                                       100|                                                                 443|                                                                                                                                                                                                                                                                                                                    
                             26                                                                        375                                                                  445
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5FPU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

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  5fpu
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  KDM5B_HUMAN | Q9UGL1
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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 5fun 5fup 5fv3 5fy4 5fy5 5fy9 5fyb 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

5fpl CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH CCT363901
5fpv CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND KDOAM20A