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(-) Description

Title :  JMJD2A IN COMPLEX WITH NI(II) AND ALPHA-KETOGLUTARATE
 
Authors :  B. Cascella, S. G. Lee, J. M. Jez
Date :  09 Nov 16  (Deposition) - 01 Feb 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase Demethylase Monooxygenase Epigenetics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Cascella, S. G. Lee, S. Singh, J. M. Jez, L. M. Mirica
The Small Molecule Jib-04 Disrupts O2 Binding In The Fe-Dependent Histone Demethylase Kdm4A/Jmjd2A.
Chem. Commun. (Camb. ) V. 53 2174 2017
PubMed-ID: 28144654  |  Reference-DOI: 10.1039/C6CC09882G

(-) 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: UNP RESIDUES 1-159
    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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2NI2Ligand/IonNICKEL (II) ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2NI-1Ligand/IonNICKEL (II) ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2NI-1Ligand/IonNICKEL (II) ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:188 , GLU A:190 , HIS A:276 , AKG A:402 , HOH A:559binding site for residue NI A 401
2AC2SOFTWARETYR A:132 , TYR A:177 , PHE A:185 , HIS A:188 , GLU A:190 , SER A:196 , ASN A:198 , LYS A:206 , TRP A:208 , HIS A:276 , SER A:288 , NI A:401 , HOH A:589binding site for residue AKG A 402
3AC3SOFTWARECYS A:234 , HIS A:240 , CYS A:306 , CYS A:308binding site for residue ZN A 403
4AC4SOFTWAREHIS B:188 , GLU B:190 , HIS B:276 , AKG B:402 , HOH B:555binding site for residue NI B 401
5AC5SOFTWARETYR B:132 , TYR B:177 , PHE B:185 , HIS B:188 , GLU B:190 , SER B:196 , ASN B:198 , LYS B:206 , HIS B:276 , SER B:288 , NI B:401 , HOH B:550binding site for residue AKG B 402
6AC6SOFTWARECYS B:234 , HIS B:240 , CYS B:306 , CYS B:308binding site for residue ZN B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TVR)

(-) 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:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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..hhhhhhhh...........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5tvr A   6 ETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345        


Chain B from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tvr B   7 TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAE 352
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346
   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 5TVR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KDM4A_HUMAN | O75164: 2gf7 2gfa 2gp3 2gp5 2oq6 2oq7 2os2 2ot7 2ox0 2p5b 2pxj 2q8c 2q8d 2q8e 2qqr 2qqs 2vd7 2wwj 2ybk 2ybp 2ybs 3njy 3pdq 3rvh 3u4s 4ai9 4bis 4gd4 4ura 4v2v 4v2w 5a7n 5a7o 5a7p 5a7q 5a7s 5a7w 5a80 5anq 5d6w 5d6x 5d6y 5f2s 5f2w 5f32 5f37 5f39 5f3c 5f3e 5f3g 5f3i 5f5i 5fpv 5fwe 5fy8 5fyc 5fyh 5fyi 5ly1 5ly2 5tvs

(-) Related Entries Specified in the PDB File

5tvs