5FYH - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE

Authors :   R. Nowak, J. Kopec, C. Johansson, A. Szykowska, F. Von Delft, C. H. Arro C. Bountra, A. Edwards, U. Oppermann

Date :   07 Mar 16 (Deposition) - 23 Mar 16 (Release) - 23 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Oxidoreductase, Jmjd2A, Kdm4A, Tca Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Nowak, J. Kopec, C. Johansson, A. Szykowska, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann
Crystal Structure Of Human Jmjd2A In Complex With Fumarate
To Be Published
PubMed: search

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4A
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 4-354
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JU MONJI DOMAIN-CONTAINING PROTEIN 2A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 12)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	FUM	2	Ligand/Ion	FUMARIC ACID
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	SO4	2	Ligand/Ion	SULFATE ION
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	FUM	1	Ligand/Ion	FUMARIC ACID
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	SO4	1	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	FUM	1	Ligand/Ion	FUMARIC ACID
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	SO4	1	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308	BINDING SITE FOR RESIDUE ZN A 502
02	AC2	SOFTWARE	CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308	BINDING SITE FOR RESIDUE ZN B 502
03	AC3	SOFTWARE	TYR A:132 , PHE A:185 , HIS A:188 , ASN A:198 , LYS A:206 , TRP A:208 , HIS A:276 , MN A:1357 , HOH A:2034 , HOH A:2037	BINDING SITE FOR RESIDUE FUM A1355
04	AC4	SOFTWARE	TYR B:132 , PHE B:185 , HIS B:188 , LYS B:206 , TRP B:208 , HIS B:276 , MN B:1356 , HOH B:2048 , HOH B:2052	BINDING SITE FOR RESIDUE FUM B1354
05	AC5	SOFTWARE	LYS A:105 , PHE B:227 , PRO B:228 , GLY B:229 , SER B:230	BINDING SITE FOR RESIDUE SO4 B1355
06	AC6	SOFTWARE	PHE A:227 , PRO A:228 , GLY A:229 , SER A:230 , LYS B:105	BINDING SITE FOR RESIDUE SO4 A1356
07	AC7	SOFTWARE	HIS A:188 , GLU A:190 , HIS A:276 , FUM A:1355 , HOH A:2034 , HOH A:2037	BINDING SITE FOR RESIDUE MN A1357
08	AC8	SOFTWARE	HIS B:188 , GLU B:190 , HIS B:276 , FUM B:1354 , HOH B:2045 , HOH B:2048	BINDING SITE FOR RESIDUE MN B1356
09	AC9	SOFTWARE	TYR B:121 , TRP B:122 , PHE B:185 , TRP B:187 , LEU B:244 , ILE B:245 , ALA B:277 , GLY B:278	BINDING SITE FOR RESIDUE EDO B1357
10	BC1	SOFTWARE	TYR B:106 , ASN B:128 , PRO B:130 , MET B:180 , TRP B:181 , LYS B:182	BINDING SITE FOR RESIDUE EDO B1358
11	BC2	SOFTWARE	SER B:246 , LEU B:248 , HOH B:2034	BINDING SITE FOR RESIDUE EDO B1359
12	BC3	SOFTWARE	TRP A:332 , LYS A:333	BINDING SITE FOR RESIDUE EDO A1358

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

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

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

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

(no "Exon" information available for 5FYH)

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
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Chain A from PDB  Type:PROTEIN  Length:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee.............hhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fyh A   4 ESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353

Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee...........hhhhh.hhhhhhh.............eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhhhhhhhhhhh............hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fyh B   7 TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    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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	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 '\|'

(no "SCOP Domain" information available for 5FYH)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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5fxv	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N05859B
5fxw	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH FUMARATE
5fxx	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH OXALOACETATE
5fxz	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH CITRATE
5fy0	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH L-MALATE
5fy1	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N08619B
5fy4	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH SUCCINATE
5fy5	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH FUMARATE
5fy7	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH SUCCINATE
5fy8	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH D- THREO-ISOCITRATE
5fy9	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH PYRUVATE
5fyb	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH MC1648
5fyc	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE
5fyi	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE
5fym	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fys	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH D-2-HYDROXYGLUTARATE
5fyt	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N09996A
5fyu	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10042A
5fyv	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH OXALOACETATE
5fyy	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N05798A
5fyz	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10063A
5fz0	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N11213A
5fz1	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH E48115B
5fz3	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N08776B
5fz4	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX WITH N10057A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (25, 25)

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