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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PLU1 IN COMPLEX WITH N-OXALYLGLYCINE.
 
Authors :  V. Srikannathasan, C. Johansson, C. Strain-Damerell, C. Gileadi, A. S K. Kupinska, J. Kopec, T. Krojer, H. Steuber, F. Von Delft, N. A. Burge C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Oppermann
Date :  29 Apr 15  (Deposition) - 06 May 15  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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, LYSINE-SPECIFIC DEMETHYLASE 5B
    Chains: A
    EC Number: 1.14.11.-, 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, JMJC DOMAIN, RESIDUES
    Gene: KDM5B, JARID1B, PLU1, RBBP2H1
    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, 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, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3MN2Ligand/IonMANGANESE (II) ION
4OGA1Ligand/IonN-OXALYLGLYCINE
5PO41Ligand/IonPHOSPHATE ION
6ZN2Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
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
03AC3SOFTWAREPHE 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 , MN A:1758 , EDO A:1765 , EDO A:1766 , HOH A:2098 , HOH A:2203BINDING SITE FOR RESIDUE OGA A1756
04AC4SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419BINDING SITE FOR RESIDUE MN A1757
05AC5SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , OGA A:1756 , HOH A:2098BINDING SITE FOR RESIDUE MN A1758
06AC6SOFTWAREHIS A:622 , LYS A:694 , HIS A:718 , HOH A:2143BINDING SITE FOR RESIDUE PO4 A1759
07AC7SOFTWAREILE A:500 , TRP A:504 , GLU A:531 , MET A:534 , LEU A:541 , 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:2096 , HOH A:2101 , HOH A:2149BINDING SITE FOR RESIDUE EPE A1760
08AC8SOFTWAREILE A:475 , ALA A:477 , PHE A:627 , SER A:628 , GLU A:631 , MET A:632 , HOH A:2184BINDING SITE FOR RESIDUE EDO A1761
09AC9SOFTWAREASP 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:2204BINDING SITE FOR RESIDUE EDO A1762
10BC1SOFTWAREVAL A:674 , ILE A:675 , HOH A:2167 , HOH A:2171BINDING SITE FOR RESIDUE EDO A1763
11BC2SOFTWAREALA 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 A1764
12BC3SOFTWARETYR A:425 , SER A:494 , SER A:495 , LYS A:517 , ASN A:591 , OGA A:1756 , HOH A:2203BINDING SITE FOR RESIDUE EDO A1765
13BC4SOFTWARETYR A:488 , GLU A:501 , ASN A:601 , OGA A:1756 , HOH A:2090 , HOH A:2098BINDING SITE FOR RESIDUE EDO A1766
14BC5SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2154BINDING SITE FOR RESIDUE EDO A1767

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A1F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A1F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A1F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A1F)

(-) Exons   (0, 0)

(no "Exon" information available for 5A1F)

(-) 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:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee.................ee..eeee......ee....eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeeeee.............hhhhhhhhhh....hhhhhh..hhhhhh...hhhhhh.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
                 5a1f A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAE 753
                             ||     33        43        53        63        73        83        93     ||378       388       398       408       418       428       438   ||  453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753
                             0|                                                                       99|                                                                442|                                                                                                                                                                                                                                                                                                                 
                             26                                                                       375                                                                 448
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5A1F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A1F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A1F)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a1f
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 Related Entries

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UniProtKB/Swiss-Prot
        KDM5B_HUMAN | Q9UGL1: 2ma5 2mny 2mnz 5a3n 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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