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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JARID1C IN COMPLEX WITH KDM5-C49
 
Authors :  V. Srikannathasan, A. Szykowska, C. Strain-Damerell, J. Kopec, R. Now C. Gileadi, C. Johansson, K. Kupinska, N. A. Burgess-Brown, L. Shrest W. Dong, F. Vondelft, C. H. Arrowsmith, C. Bountra, A. Edwards, K. Hube U. Oppermann
Date :  17 Feb 16  (Deposition) - 13 Apr 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Lysine-Specific, Lysine-Specific Demethylase 5C (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 - HISTONE DEMETHYLASE JARID1C
    Chains: A, B
    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 8-83 AND 384-772
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)(ETHYL) AMINO)-2-OXOETHYL)AMINO)METHYL) ISONICOTINIC ACID)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2MMK2Ligand/Ion2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL)AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4-CARBOXYLIC ACID
3MN2Ligand/IonMANGANESE (II) ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MMK1Ligand/Ion2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL)AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4-CARBOXYLIC ACID
3MN-1Ligand/IonMANGANESE (II) ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MMK1Ligand/Ion2-{[(2-{[(E)-2-(DIMETHYLAMINO)ETHENYL](ETHYL)AMINO}-2-OXOETHYL)AMINO]METHYL}PYRIDINE-4-CARBOXYLIC ACID
3MN-1Ligand/IonMANGANESE (II) ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:707 , CYS A:710 , CYS A:730 , HIS A:733BINDING SITE FOR RESIDUE ZN A1770
02AC2SOFTWARECYS A:721 , CYS A:724 , CYS A:738 , CYS A:740BINDING SITE FOR RESIDUE ZN A1771
03AC3SOFTWAREHIS A:514 , GLU A:516 , HIS A:602 , MMK A:1775 , HOH A:2183BINDING SITE FOR RESIDUE MN A1772
04AC4SOFTWAREARG A:627 , GLN A:628 , ALA B:541 , HIS B:544BINDING SITE FOR RESIDUE MG A1773
05AC5SOFTWAREHOH A:2067 , HOH A:2068 , HOH A:2069 , HOH A:2317BINDING SITE FOR RESIDUE MG A 805
06AC6SOFTWAREARG A:627 , LYS A:668 , HOH A:2279 , PRO B:538BINDING SITE FOR RESIDUE MG A1774
07AC7SOFTWARETYR A:440 , ASP A:443 , GLY A:496 , TRP A:501 , TYR A:503 , PHE A:511 , HIS A:514 , GLU A:516 , ASN A:524 , LYS A:532 , TRP A:534 , HIS A:602 , VAL A:615 , ASN A:616 , MN A:1772 , HOH A:2183 , HOH A:2319BINDING SITE FOR RESIDUE MMK A1775
08AC8SOFTWARECYS B:707 , CYS B:710 , CYS B:730 , HIS B:733BINDING SITE FOR RESIDUE ZN B1770
09AC9SOFTWARECYS B:721 , CYS B:724 , CYS B:738 , CYS B:740BINDING SITE FOR RESIDUE ZN B1771
10BC1SOFTWAREHIS B:514 , GLU B:516 , HIS B:602 , MMK B:1775 , HOH B:2138BINDING SITE FOR RESIDUE MN B1772
11BC2SOFTWAREARG B:634 , ARG B:637 , HIS B:733BINDING SITE FOR RESIDUE MG B1773
12BC3SOFTWAREPRO B:624 , ARG B:627 , LYS B:668 , HOH B:2198 , HOH B:2287BINDING SITE FOR RESIDUE MG B1774
13BC4SOFTWARETYR B:440 , ASP B:443 , TRP B:501 , TYR B:503 , PHE B:511 , HIS B:514 , GLU B:516 , LYS B:532 , TRP B:534 , HIS B:602 , VAL B:615 , ASN B:616 , MN B:1772 , HOH B:2138 , HOH B:2288BINDING SITE FOR RESIDUE MMK B1775

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FWJ)

(-) Sequences/Alignments

Asymmetric 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:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee............hhhh.ee..eeee.......eehhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......eeeeeeeeehhhhh............hhhhhhhhhh.....hhhhh..hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhh..hhhhhhh.....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhh...........eeeee........hhhhh......hhh.eeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fwj A   6 SMFLPPPECPVFEPSWAEFRDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEVDNFRFTPRIQRLNELTREYTLQSFGEMADSFKADYFNMPVHMVPTELVEKEFWRLVNSIEEDVTVEYGADIHSKEFGSGFPVSDSKRHLTPEEEEYATSGWNLNVMPVLEQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMKKLTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYNFAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAACPEKLDLNLAAAVHKEMFIMVQEERRLRKALLEKGITEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPAMLHKLKVRAES 769
                                    15        25        35        45        55        65        75|      398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548    || 574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764     
                                                                                                75|                                                                                                                                                                 553|                                                                                                                                                                                                       
                                                                                                389                                                                                                                                                                  570                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..hhhhhhhhhhhhhhhhhhhh...eeee............hhhh.ee..eeee.......eehhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......eeeeeeeeehhhhh......hhhhhhhhhh.....hhhhh..hhhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhhh..hhhhhhh.....eeeee....eeee.....eeeee...eeeeeeee.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh...........eeeee........hhhhh......hhh.eeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fwj B   6 SMFLPPPECPVFEPSWAEFRDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEVDNFRFTPRIQRLNELTREYTLQSFGEMADSFKADYFNMPVHMVPTELVEKEFWRLVNSIEEDVTVEYGADIHSKEFGSGFPVSTPEEEEYATSGWNLNVMPVLEQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMKKLTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYNFAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAACPEKLDLNLAAAVHKEMFIMVQEERRLRKALLEKGITEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPAMLHKLKVRAES 769
                                    15        25        35        45        55        65        75|      398       408       418       428       438       448       464       474       484       494       504       514       524       534       544       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760         
                                                                                                75|                                                                456|                                                                                       553|                                                                                                                                                                                                       
                                                                                                389                                                                 463                                                                                        570
   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 5FWJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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        KDM5C_HUMAN | P41229: 2jrz

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