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(-) Description

Title :  CRYSTAL STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR
 
Authors :  O. N. F. King, T. Krojer, C. H. Arrowsmith, A. Edwards, C. Bountra, M. A. M C. J. Schofield, Structural Genomics Consortium (Sgc)
Date :  31 Jul 12  (Deposition) - 15 Aug 12  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase, Jmjc Domain, Chromatin Regulator, Dioxygenase, Transcription, Demethylation, Iron, 2-Oxoglutarate, Alpha- Ketoglutarate, Nucleus, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. N. F. King, T. Krojer, Arrowsmith C. H. , Edwards A. , Bountra C. , M. A. Mcdonough, C. J. Schofield, Structural Genomics Consortium (Sgc)
Crystal Structure Of Jmjd2A Complexed With Inhibitor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4A
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN
    Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JUMONJI DOMAIN-CONTAINING PROTEIN 2A

 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, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
10WS2Ligand/Ion2-(1H-PYRAZOL-3-YL)PYRIDINE-4-CARBOXYLIC ACID
2CL4Ligand/IonCHLORIDE ION
3NI2Ligand/IonNICKEL (II) ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10WS1Ligand/Ion2-(1H-PYRAZOL-3-YL)PYRIDINE-4-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3NI-1Ligand/IonNICKEL (II) ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10WS1Ligand/Ion2-(1H-PYRAZOL-3-YL)PYRIDINE-4-CARBOXYLIC ACID
2CL-1Ligand/IonCHLORIDE ION
3NI-1Ligand/IonNICKEL (II) ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:188 , GLU A:190 , HIS A:276 , 0WS A:504 , HOH A:739BINDING SITE FOR RESIDUE NI A 501
02AC2SOFTWARECYS A:234 , HIS A:240 , CYS A:306 , CYS A:308BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREGLU A:235 , ALA A:236 , PHE A:237 , LEU A:238BINDING SITE FOR RESIDUE CL A 503
04AC4SOFTWARETYR A:132 , TYR A:177 , PHE A:185 , HIS A:188 , GLU A:190 , LYS A:206 , TRP A:208 , LYS A:241 , HIS A:276 , NI A:501 , HOH A:642 , HOH A:739BINDING SITE FOR RESIDUE 0WS A 504
05AC5SOFTWAREHIS B:188 , GLU B:190 , HIS B:276 , 0WS B:506 , HOH B:728BINDING SITE FOR RESIDUE NI B 501
06AC6SOFTWARECYS B:234 , HIS B:240 , CYS B:306 , CYS B:308BINDING SITE FOR RESIDUE ZN B 502
07AC7SOFTWAREARG B:98BINDING SITE FOR RESIDUE CL B 503
08AC8SOFTWAREGLU B:113 , GLU B:116 , ARG B:119BINDING SITE FOR RESIDUE CL B 504
09AC9SOFTWAREPHE B:237 , LYS B:241 , MET B:242 , THR B:243BINDING SITE FOR RESIDUE CL B 505
10BC1SOFTWARETYR B:132 , TYR B:177 , PHE B:185 , HIS B:188 , GLU B:190 , LYS B:206 , TRP B:208 , LYS B:241 , NI B:501 , HOH B:647 , HOH B:728BINDING SITE FOR RESIDUE 0WS B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GD4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GD4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GD4)

(-) Exons   (0, 0)

(no "Exon" information available for 4GD4)

(-) 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:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4gd4a_ A: JMJD2A core                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gd4 A   5 SETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354


Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gd4b_ B: JMJD2A core                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gd4 B   8 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GD4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GD4)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

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