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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDOAM25A
 
Authors :  V. Srikannathasan, C. Johansson, C. Gileadi, A. Nuzzi, G. F. Ruda, J. Ko Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, P. Brennan, U. Opperm
Date :  02 Jun 15  (Deposition) - 08 Jul 15  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Tumber, A. Nuzzi, E. S. Hookway, S. B. Hatch, S. Velupillai, C. Johansson, A. Kawamura, P. Savitsky, C. Yapp, A. Szykowska, N. Wu, C. Bountra, C. Strain-Damerell, N. A. Burgess-Brown, G. F. Ruda, O. Fedorov, S. Munro, K. S. England, R. P. Nowak, C. J. Schofield, N. B. La Thangue, C. Pawlyn, F. Davies, G. Morgan, N. Athanasou, S. Muller, U. Oppermann, P. E. Brennan
Potent And Selective Kdm5 Inhibitor Stops Cellular Demethylation Of H3K4Me3 At Transcription Start Sites And Proliferation Of Mm1S Myeloma Cells.
Cell Chem Biol V. 24 371 2017
PubMed-ID: 28262558  |  Reference-DOI: 10.1016/J.CHEMBIOL.2017.02.006

(-) 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  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4LQT1Ligand/Ion2-[[[2-[2-(DIMETHYLAMINO)ETHYL-ETHYL-AMINO]-2-OXIDANYLIDENE-ETHYL]AMINO]METHYL]PYRIDINE-4-CARBOXAMIDE
5MN3Ligand/IonMANGANESE (II) ION
6PO41Ligand/IonPHOSPHATE ION
7ZN2Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:692 , CYS A:695 , CYS A:715 , HIS A:718BINDING SITE FOR RESIDUE ZN A 1754
02AC2SOFTWARECYS A:706 , CYS A:708 , CYS A:723 , CYS A:725BINDING SITE FOR RESIDUE ZN A 1755
03AC3SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419BINDING SITE FOR RESIDUE MN A 1756
04AC4SOFTWAREGLU A:678 , ARG A:735 , HOH A:2399BINDING SITE FOR RESIDUE MN A 1757
05AC5SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , LQT A:1759 , HOH A:2210BINDING SITE FOR RESIDUE MN A 1758
06AC6SOFTWAREARG A:98 , TYR A:425 , TRP A:486 , 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:1758 , DMS A:1760 , HOH A:2100 , HOH A:2210 , HOH A:2216 , HOH A:2230BINDING SITE FOR RESIDUE LQT A 1759
07AC7SOFTWAREARG A:98 , TYR A:425 , TYR A:488 , LQT A:1759 , HOH A:2100 , HOH A:2400BINDING SITE FOR RESIDUE DMS A 1760
08AC8SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2300 , HOH A:2304BINDING SITE FOR RESIDUE PO4 A 1761
09AC9SOFTWAREILE A:500 , TRP A:504 , GLU A:531 , MET A:534 , LEU A:541 , PHE A:542 , LEU A:552 , VAL A:553 , TYR A:586 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2203 , HOH A:2204 , HOH A:2209 , HOH A:2253 , HOH A:2401BINDING SITE FOR RESIDUE EPE 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:713 , HOH A:2403BINDING SITE FOR RESIDUE EDO A 1763
11BC2SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2336 , HOH A:2345BINDING SITE FOR RESIDUE EDO A 1764
12BC3SOFTWAREALA A:386 , ASP A:387 , LYS A:390 , MET A:491 , CYS A:492 , GLU A:515 , GLY A:593 , PHE A:594BINDING SITE FOR RESIDUE EDO A 1765
13BC4SOFTWAREPHE A:74 , ALA A:75 , CYS A:76 , GLY A:435 , SER A:436BINDING SITE FOR RESIDUE EDO A 1766
14BC5SOFTWAREHOH A:2369BINDING SITE FOR RESIDUE EDO A 1767
15BC6SOFTWARELYS A:639 , GLU A:678 , LYS A:731 , HOH A:2404BINDING SITE FOR RESIDUE EDO A 1768

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A3N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A3N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A3N)

(-) Exons   (0, 0)

(no "Exon" information available for 5A3N)

(-) 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:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee.....eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeee..ee..................hhhhhhh........hhhhh...........hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh........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
                 5a3n A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93      |377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747      
                             0|                                                                       100|                                                                                                                                                                                                                                                                                                                                                                                          
                             26                                                                        375
   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 5A3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A3N)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a3n
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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 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 5fzd 5fze 5fzf 5fzg 5fzh 5fzi 5fzk 5fzl 5fzm 5lw9 5lwb

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