5FY0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH L-MALATE

Authors :   R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, F. Von Delf C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann

Date :   03 Mar 16 (Deposition) - 16 Mar 16 (Release) - 16 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

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

Keywords :   Transferase, Trasnferase, Tca Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann
Crystal Structure Of Jmjc Domain Of Human Histone Demethylase Uty In Complex With L-Malate
To Be Published
PubMed: search

Molecule 1 - HISTONE DEMETHYLASE UTY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Fragment	:	JMJC DOMAIN, RESIDUES 878-1347
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME, U BIQUITOUSLY-TRANSCRIBED Y CHROMOSOME TETRATRICOPEPTIDE REPEAT PROTEIN

		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 (4, 21)

No.	Name	Count	Type	Full Name
1	EDO	15	Ligand/Ion	1,2-ETHANEDIOL
2	LMR	2	Ligand/Ion	(2S)-2-HYDROXYBUTANEDIOIC ACID
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	LMR	1	Ligand/Ion	(2S)-2-HYDROXYBUTANEDIOIC ACID
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	LMR	1	Ligand/Ion	(2S)-2-HYDROXYBUTANEDIOIC ACID
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:1278 , CYS A:1281 , CYS A:1305 , CYS A:1308	BINDING SITE FOR RESIDUE ZN A4002
02	AC2	SOFTWARE	CYS B:1278 , CYS B:1281 , CYS B:1305 , CYS B:1308	BINDING SITE FOR RESIDUE ZN B4002
03	AC3	SOFTWARE	HIS B:1093 , GLU B:1095 , HIS B:1173 , HOH B:2130 , HOH B:2137 , LMR B:2346	BINDING SITE FOR RESIDUE MN B2345
04	AC4	SOFTWARE	HIS A:1093 , GLU A:1095 , HIS A:1173 , HOH A:2142 , HOH A:2150 , LMR A:2346 , EDO A:2353	BINDING SITE FOR RESIDUE MN A2345
05	AC5	SOFTWARE	TYR B:1082 , LYS B:1084 , THR B:1090 , HIS B:1093 , ASN B:1103 , TRP B:1113 , HIS B:1173 , ASN B:1183 , HOH B:2123 , HOH B:2125 , HOH B:2137 , MN B:2345	BINDING SITE FOR RESIDUE LMR B2346
06	AC6	SOFTWARE	TYR A:1082 , LYS A:1084 , THR A:1090 , HIS A:1093 , ASN A:1103 , TRP A:1113 , HIS A:1173 , VAL A:1175 , ASN A:1183 , HOH A:2137 , HOH A:2150 , MN A:2345	BINDING SITE FOR RESIDUE LMR A2346
07	AC7	SOFTWARE	ILE B:967 , TRP B:968 , ARG B:969 , ASN B:1131	BINDING SITE FOR RESIDUE EDO B2347
08	AC8	SOFTWARE	SER A:932 , THR A:933 , GLN A:986 , PRO A:1108 , ASN A:1182 , EDO A:2348 , EDO A:2352	BINDING SITE FOR RESIDUE EDO A2347
09	AC9	SOFTWARE	PHE A:990 , HOH A:2073 , EDO A:2347	BINDING SITE FOR RESIDUE EDO A2348
10	BC1	SOFTWARE	ARG A:1156 , HOH A:2004 , GLU B:999	BINDING SITE FOR RESIDUE EDO A2349
11	BC2	SOFTWARE	HIS A:1267 , GLU A:1273 , HIS A:1276 , TYR A:1301	BINDING SITE FOR RESIDUE EDO A2350
12	BC3	SOFTWARE	GLY A:919 , GLY A:922 , PRO A:1161 , GLY A:1162 , ASP A:1163 , HOH A:2179 , HOH A:2306 , HOH A:2307	BINDING SITE FOR RESIDUE EDO A2351
13	BC4	SOFTWARE	LYS A:895 , VAL B:1123 , ASP B:1126 , PHE B:1127 , HOH B:2280	BINDING SITE FOR RESIDUE EDO B2348
14	BC5	SOFTWARE	PHE B:990 , PRO B:1108 , TRP B:1180 , HOH B:2073 , HOH B:2281 , EDO B:2350	BINDING SITE FOR RESIDUE EDO B2349
15	BC6	SOFTWARE	THR B:933 , GLN B:986 , PRO B:1108 , ASN B:1182 , EDO B:2349	BINDING SITE FOR RESIDUE EDO B2350
16	BC7	SOFTWARE	LEU A:928 , GLY A:929 , SER A:932 , ILE A:1106 , GLY A:1107 , HOH A:2155 , EDO A:2347	BINDING SITE FOR RESIDUE EDO A2352
17	BC8	SOFTWARE	LEU B:1050 , ARG B:1058 , VAL B:1059 , VAL B:1060 , HOH B:2104 , HOH B:2114	BINDING SITE FOR RESIDUE EDO B2351
18	BC9	SOFTWARE	GLY A:1075 , GLU A:1095 , TRP A:1186 , ASN A:1187 , HOH A:2142 , MN A:2345	BINDING SITE FOR RESIDUE EDO A2353
19	CC1	SOFTWARE	HIS B:943 , ASP B:1036 , ASP B:1039 , HOH B:2038	BINDING SITE FOR RESIDUE EDO B2352
20	CC2	SOFTWARE	LYS B:1207 , CYS B:1281 , GLU B:1282 , VAL B:1283 , HOH B:2186	BINDING SITE FOR RESIDUE EDO B2353
21	CC3	SOFTWARE	GLY B:1075 , GLN B:1080 , TYR B:1082 , GLU B:1095 , SER B:1101 , ASN B:1187 , HOH B:2122 , HOH B:2123 , HOH B:2130 , HOH B:2137	BINDING SITE FOR RESIDUE EDO B2354

(no "SS Bond" information available for 5FY0)

Asymmetric Unit

No.	Residues
1	Gly A:1024	-	Pro A:1025
2	Gly A:1107	-	Pro A:1108
3	Gly B:1107	-	Pro B:1108

(no "SAP(SNP)/Variant" information available for 5FY0)

(no "PROSITE Motif" information available for 5FY0)

(no "Exon" information available for 5FY0)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhh........eeeeeeeee......hhhhhhhhhhhhhhhh......hhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5fy0 A  880 KDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKRKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLS 1344
                                   889       899       909       919       929       939       949       959       969       979       989       999 ||   1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340    
                                                                                                                                                  1001|                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                   1023

Chain B from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeee......hhhhhhhhhhhhhhhh......hhhhh..........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.........ee......ee..eeeeehhhhhh......hhhhhhhhh.....eeeee..hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fy0 B  881 DKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLS 1344
                                   890       900       910       920       930       940       950       960       970       980       990      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335         
                                                                                                                                                999|                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                1025

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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 5FY0)

(no "CATH Domain" information available for 5FY0)

(no "Pfam Domain" information available for 5FY0)

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Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:1024 - Pro A:1025	[ RasMol ]
		Gly A:1107 - Pro A:1108	[ RasMol ]
		Gly B:1107 - Pro B:1108	[ RasMol ]

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	UTY_HUMAN \| O14607	:	3zli 3zpo 4uf0 5a1l 5fxv 5fxw 5fxx 5fxz 5fy1 5fy7 5fym

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
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
5fyh	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE
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

Description

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Ligands, Modified Residues, Ions (4, 21)

Sites (21, 21)

SS Bonds (0, 0)

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