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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JARID1B IN COMPLEX WITH 2-OXOGLUTARATE.
 
Authors :  R. Nowak, V. Srikannathasan, C. Johansson, C. Gileadi, K. Kupinska, C. Strain- Damerell, A. Szykowska, R. Talon, F. Von Delft, N. A. Burgess-Brown, C. H. Arrowsmith, C. Bountra, A. M. Edwards, U. Op
Date :  28 Jan 16  (Deposition) - 23 Mar 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
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
    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 TO 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, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2CL1Ligand/IonCHLORIDE ION
3EDO9Ligand/Ion1,2-ETHANEDIOL
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
5MN2Ligand/IonMANGANESE (II) ION
6ZN2Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
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
03AC3SOFTWAREHIS A:499 , GLU A:501 , HIS A:587 , AKG A:1764 , HOH A:2252BINDING SITE FOR RESIDUE MN A1757
04AC4SOFTWAREHOH A:2456BINDING SITE FOR RESIDUE MN A1758
05AC5SOFTWAREILE A:500 , TRP A:504 , LEU A:541 , LEU A:552 , VAL A:553 , TYR A:586 , HIS A:617 , TYR A:618 , LEU A:621 , ARG A:623 , HOH A:2250 , HOH A:2256 , HOH A:2289 , HOH A:2318 , HOH A:2360 , HOH A:2482BINDING SITE FOR RESIDUE EPE A1759
06AC6SOFTWARELEU A:90 , ASN A:91 , LEU A:413 , THR A:416 , GLU A:419 , HOH A:2111BINDING SITE FOR RESIDUE CL A1762
07AC7SOFTWAREASP A:630 , CYS A:699 , PHE A:700 , MET A:701 , SER A:702 , HOH A:2369BINDING SITE FOR RESIDUE EDO A2760
08AC8SOFTWARETYR A:734 , HOH A:2468 , HOH A:2485BINDING SITE FOR RESIDUE EDO A2762
09AC9SOFTWAREARG A:612 , ASP A:630 , MET A:658 , ASP A:661 , GLU A:662 , HOH A:2455BINDING SITE FOR RESIDUE EDO A2763
10BC1SOFTWAREPRO A:30 , VAL A:568BINDING SITE FOR RESIDUE EDO A2764
11BC2SOFTWAREASP 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:2488BINDING SITE FOR RESIDUE EDO A2765
12BC3SOFTWAREGLY A:524 , TYR A:525 , ARG A:584 , HOH A:2277 , HOH A:2489BINDING SITE FOR RESIDUE EDO A2766
13BC4SOFTWAREARG A:670 , VAL A:674 , ILE A:675 , HOH A:2179 , HOH A:2397BINDING SITE FOR RESIDUE EDO A2767
14BC5SOFTWARETRP A:70 , GLU A:453 , SER A:457 , HOH A:2039BINDING SITE FOR RESIDUE EDO A2768
15BC6SOFTWARETYR A:488 , GLU A:501 , ALA A:599 , ASN A:601 , AKG A:1764 , HOH A:2234 , HOH A:2252 , HOH A:2490BINDING SITE FOR RESIDUE EDO A2769
16BC7SOFTWARETYR A:425 , TYR 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 , MN A:1757 , HOH A:2252 , HOH A:2483 , EDO A:2769BINDING SITE FOR RESIDUE AKG A1764

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FUP)

(-) 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......hhhhhhhhhhhhhhh.....eeeeeeee................hhhhhhh........hhhhh..hhhhh....hhhhhh.eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhhhhhhh...hhhh.ee...hhhhhhhh....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh...........eeeee...........hhhhh...hhh.eeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fup A  -1 SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVRDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAES 754
                             ||     33        43        53        63        73        83        93     ||378       388       398       408       418       428       438   ||  450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750    
                             0|                                                                       99|                                                                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 5FUP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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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 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

5fv3 CRYSTAL STRUCTURE OF HUMAN JARID1B CONSTRUCT C2 IN COMPLEX WITH N-OXALYLGLYCINE.