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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)(ETHYL)AMINO)-2-OXOETHYL)AMINO)METHYL) ISONICOTINIC ACID).
 
Authors :  V. Srikannathasan, C. Johansson, C. Gileadi, J. Kopec, C. Strain-Dame K. Kupinska, N. A. Burgessbrown, F. Von Delft, C. H. Arrowsmith, C. Bo A. M. Edwards, U. Oppermann
Date :  02 Jun 15  (Deposition) - 17 Jun 15  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, 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
    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 26-101,374-772
    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  (6, 12)

Asymmetric/Biological Unit (6, 12)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3MMK1Ligand/Ion2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL)AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4-CARBOXYLIC ACID
4MN1Ligand/IonMANGANESE (II) ION
5NI1Ligand/IonNICKEL (II) ION
6ZN1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A1754
02AC2SOFTWAREILE A:500 , TRP A:504 , LEU A:541 , PHE A:542 , LEU A:552 , VAL A:553 , ARG A:584 , TYR A:586 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2117 , HOH A:2123 , HOH A:2150 , HOH A:2241BINDING SITE FOR RESIDUE EPE A1755
03AC3SOFTWAREARG A:98 , TYR A:425 , ASP A:428 , TYR A:488 , PHE A:496 , HIS A:499 , GLU A:501 , LYS A:517 , TRP A:519 , HIS A:587 , VAL A:600 , ASN A:601 , MN A:1765 , HOH A:2051 , HOH A:2124 , HOH A:2129 , HOH A:2242BINDING SITE FOR RESIDUE MMK A1756
04AC4SOFTWAREHIS A:622 , HIS A:718BINDING SITE FOR RESIDUE NI A1757
05AC5SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2184BINDING SITE FOR RESIDUE EDO A1758
06AC6SOFTWAREARG A:666 , THR A:737 , HOH A:2234BINDING SITE FOR RESIDUE EDO A1759
07AC7SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , ASP A:420 , VAL A:421 , HOH A:2087BINDING SITE FOR RESIDUE EDO A1760
08AC8SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , HOH A:2168BINDING SITE FOR RESIDUE EDO A1761
09AC9SOFTWAREPRO A:465 , SER A:470 , LEU A:472 , MET A:482 , ASN A:601 , PHE A:602 , CYS A:603BINDING SITE FOR RESIDUE EDO A1762
10BC1SOFTWAREGLU A:468 , SER A:470 , VAL A:471 , LEU A:472 , ALA A:473 , HIS A:474 , MET A:636 , LEU A:643 , VAL A:647 , HOH A:2103BINDING SITE FOR RESIDUE EDO A1763
11BC2SOFTWAREASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , VAL A:693 , LEU A:712 , LEU A:713BINDING SITE FOR RESIDUE EDO A1764
12BC3SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , MMK A:1756 , HOH A:2124BINDING SITE FOR RESIDUE MN A1765

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:706 -A:723
2A:708 -A:725

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A3T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A3T)

(-) Exons   (0, 0)

(no "Exon" information available for 5A3T)

(-) 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:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee.....eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeehhhhh..........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
                 5a3t A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93      |377       387       397       407       417       427       437    || 449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749    
                             0|                                                                       100|                                                                442|                                                                                                                                                                                                                                                                                                                    
                             26                                                                        375                                                                 445
   Legend:   → Mismatch (orange background)
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5A3T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A3T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A3T)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a3t
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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 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 5fzd 5fze 5fzf 5fzg 5fzh 5fzi 5fzk 5fzl 5fzm 5lw9 5lwb

(-) Related Entries Specified in the PDB File

5a3n CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDOAM25A
5a3w CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH PYRIDINE-2,6-DICARBOXYLIC ACID (PDCA)