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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN PLU1 (JARID1B).
 
Authors :  R. Nowak, V. Srikannathasan, C. Johansson, C. Gileadi, C. Tallant, K. K C. Strain-Damerell, A. Szykowska, F. Von Delft, N. A. Burgess-Brown C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Date :  02 Jun 15  (Deposition) - 10 Jun 15  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase (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, UNP 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, 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  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3MN3Ligand/IonMANGANESE (II) ION
4ZN2Ligand/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 A1755
02AC2SOFTWARECYS A:706 , CYS A:708 , CYS A:723 , CYS A:725BINDING SITE FOR RESIDUE ZN A1756
03AC3SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2129BINDING SITE FOR RESIDUE MN A1757
04AC4SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , HOH A:2285 , HOH A:2286 , HOH A:2291BINDING SITE FOR RESIDUE MN A1758
05AC5SOFTWAREHIS A:622 , HOH A:2499BINDING SITE FOR RESIDUE MN A1759
06AC6SOFTWAREILE A:500 , TRP A:504 , GLU A:531 , MET A:534 , LEU A:541 , PHE A:542 , LEU A:552 , TYR A:586 , HIS A:617 , TYR A:618 , ARG A:623 , HOH A:2281 , HOH A:2290 , HOH A:2332 , HOH A:2367 , HOH A:2404 , HOH A:2532BINDING SITE FOR RESIDUE EPE A1760
07AC7SOFTWARETRP A:486 , TYR A:488 , ALA A:599 , VAL A:600 , HOH A:2286BINDING SITE FOR RESIDUE EDO A1761
08AC8SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2412BINDING SITE FOR RESIDUE EDO A1762
09AC9SOFTWAREGLY A:426 , ALA A:427 , ASP A:428 , PHE A:434 , LEU A:487 , VAL A:489 , HOH A:2209BINDING SITE FOR RESIDUE EDO A1763
10BC1SOFTWAREARG A:666 , LEU A:732 , TYR A:734 , THR A:737 , HOH A:2515 , HOH A:2534BINDING SITE FOR RESIDUE EDO A1764
11BC2SOFTWAREARG A:612 , ASP A:630 , MET A:658 , GLU A:662 , LEU A:665 , HOH A:2401BINDING SITE FOR RESIDUE EDO A1765
12BC3SOFTWAREPRO A:30 , VAL A:568BINDING SITE FOR RESIDUE EDO A1766
13BC4SOFTWAREASP A:688 , GLU A:689 , ARG A:690 , GLN A:691 , VAL A:693 , GLY A:711 , LEU A:713 , HOH A:2538BINDING SITE FOR RESIDUE EDO A1767
14BC5SOFTWAREGLY A:524 , TYR A:525 , ARG A:584 , HOH A:2320 , HOH A:2539BINDING SITE FOR RESIDUE EDO A1768
15BC6SOFTWAREVAL A:674 , ILE A:675 , HOH A:2201 , HOH A:2438BINDING SITE FOR RESIDUE EDO A1769
16BC7SOFTWARETYR A:425 , SER A:494 , SER A:495 , ASN A:591 , HOH A:2208 , HOH A:2316 , HOH A:2540BINDING SITE FOR RESIDUE EDO A1770
17BC8SOFTWARETRP A:39 , TRP A:70 , SER A:457 , HOH A:2049BINDING SITE FOR RESIDUE EDO A1771

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A3P)

(-) Exons   (0, 0)

(no "Exon" information available for 5A3P)

(-) 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......hhhhhhhhhhhhhhh.....eeeeeeee................hhhhhhh.......hhhhhh..hhhhh....hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.ee...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
                 5a3p A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAES 754
                             ||     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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    → 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 5A3P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A3P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A3P)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a3p
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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 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 5fzd 5fze 5fzf 5fzg 5fzh 5fzi 5fzk 5fzl 5fzm 5lw9 5lwb

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