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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JARID1B CONSTRUCT C2 IN COMPLEX WITH N-OXALYLGLYCINE.
 
Authors :  R. Nowak, V. Srikannathasan, C. Johansson, C. Gileadi, K. Kupinska, C. Strain-Damerell, A. Szykowska, R. Talon, F. Von Delft, N. A. Burge C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Date :  02 Feb 16  (Deposition) - 17 Feb 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Jarid1B, Plu1 (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, 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, JMJC DOMAIN, RESIDUES 374-770
    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  (7, 17)

Asymmetric/Biological Unit (7, 17)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3EDO9Ligand/Ion1,2-ETHANEDIOL
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
5MN2Ligand/IonMANGANESE (II) ION
6OGA1Ligand/IonN-OXALYLGLYCINE
7ZN1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A1754
02AC2SOFTWAREGLU A:631 , LYS A:635 , GLU A:683 , TYR A:736 , HOH A:2044BINDING SITE FOR RESIDUE DMS A1755
03AC3SOFTWARETRP A:486 , TYR A:488 , VAL A:600 , ASN A:601 , OGA A:1770 , HOH A:2054BINDING SITE FOR RESIDUE DMS A1756
04AC4SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , OGA A:1770 , HOH A:2054BINDING SITE FOR RESIDUE MN A1757
05AC5SOFTWAREHIS A:622 , HIS A:718 , HOH A:2110BINDING SITE FOR RESIDUE MN A1758
06AC6SOFTWAREILE A:500 , TRP A:504 , LEU A:541 , PHE A:542 , LEU A:552 , VAL A:553 , TYR A:586 , HIS A:617 , TYR A:618 , ARG A:623 , HOH A:2051 , HOH A:2057 , HOH A:2063BINDING SITE FOR RESIDUE EPE A1759
07AC7SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , EDO A:1762 , HOH A:2079BINDING SITE FOR RESIDUE EDO A1760
08AC8SOFTWAREARG A:666 , LEU A:732 , TYR A:734 , THR A:737 , HOH A:2091BINDING SITE FOR RESIDUE EDO A1761
09AC9SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , EDO A:1760BINDING 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 , ARG A:584 , HOH A:2120BINDING SITE FOR RESIDUE EDO A1765
13BC4SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2090 , HOH A:2093BINDING SITE FOR RESIDUE EDO A1766
14BC5SOFTWARETRP A:70 , SER A:457BINDING SITE FOR RESIDUE EDO A1767
15BC6SOFTWARETYR A:425 , TYR A:488 , SER A:494 , LYS A:517 , ASN A:591 , OGA A:1770 , HOH A:2047BINDING SITE FOR RESIDUE EDO A1768
16BC7SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2020BINDING SITE FOR RESIDUE CL A1769
17BC8SOFTWARETYR 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 , DMS A:1756 , MN A:1757 , EDO A:1768 , HOH A:2054BINDING SITE FOR RESIDUE OGA A1770

(-) 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 5FV3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FV3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FV3)

(-) Exons   (0, 0)

(no "Exon" information available for 5FV3)

(-) 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................hhhhhhh........hhhhh...........hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhh...........eeeee...........hhhhh...hhh.eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fv3 A  -1 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     
                             0|                                                                        101|                                                                442|                                                                                                                                                                                                                                                                                                                    
                             26                                                                         375                                                                 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 5FV3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FV3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FV3)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5fv3
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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 5fpu 5fun 5fup 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

5fup CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH 2- OXOGLUTARATE.