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PDBsum entry 5fyc
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Oxidoreductase
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PDB id
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5fyc
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Crystal structure of human jmjd2a in complex with succinate
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Structure:
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Lysine-specific demethylase 4a. Chain: a, b. Fragment: residues 4-354. Synonym: jmjc domain-containing histone demethylation protein 3a, jumonji domain-containing protein 2a. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.
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Resolution:
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2.26Å
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R-factor:
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0.189
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R-free:
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0.229
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Authors:
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R.Nowak,J.Kopec,C.Johansson,A.Szykowska,F.Von Delft,C.H.Arrowsmith, C.Bountra,A.Edwards,U.Oppermann
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Key ref:
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R.Nowak
et al.
Crystal structure of human jmjd2a in complex with suc.
To be published,
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Date:
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07-Mar-16
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Release date:
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16-Mar-16
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PROCHECK
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Headers
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References
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O75164
(KDM4A_HUMAN) -
Lysine-specific demethylase 4A from Homo sapiens
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Seq:
Struc:
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1064 a.a.
346 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class 2:
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E.C.1.14.11.66
- [histone H3]-trimethyl-L-lysine(9) demethylase.
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Reaction:
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N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 2-oxoglutarate + 2 O2 = N6-methyl-L-lysyl9-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
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N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3]
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+
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2
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2-oxoglutarate
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+
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2
×
O2
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=
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N(6)-methyl-L-lysyl(9)-[histone H3]
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+
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2
×
formaldehyde
Bound ligand (Het Group name = )
matches with 50.00% similarity
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+
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2
×
succinate
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+
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2
×
CO2
Bound ligand (Het Group name = )
corresponds exactly
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Enzyme class 3:
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E.C.1.14.11.69
- [histone H3]-trimethyl-L-lysine(36) demethylase.
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Reaction:
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N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 2 2-oxoglutarate + 2 O2 = N6-methyl-L-lysyl36-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
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N(6),N(6),N(6)-trimethyl-L-lysyl(36)-[histone H3]
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+
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2
×
2-oxoglutarate
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+
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2
×
O2
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=
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N(6)-methyl-L-lysyl(36)-[histone H3]
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+
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2
×
formaldehyde
Bound ligand (Het Group name = )
matches with 50.00% similarity
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+
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2
×
succinate
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+
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2
×
CO2
Bound ligand (Het Group name = )
corresponds exactly
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Links
