5FXV - JenaLib

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Title :   CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N05859B

Authors :   R. Nowak, T. Krojer, C. Johansson, C. Gileadi, K. Kupinska, V. Srikanna S. Oerum, N. M. Pearce, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. E U. Oppermann

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

Method :   X-RAY DIFFRACTION

Resolution :   1.91

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

Keywords :   Transferase, Pandda, Fragment Soaking, X-Ray Fragment Screening (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Nowak, K. Tobias, C. Johansson, C. Gileadi, K. Kupinska, V. Srikannathasan, S. Oerum, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann, C. Bountra, A. Edwards, P. Brennan, U. Oppermann
Crystal Structure Of Jmjc Domain Of Human Histone Demethylase Uty In Complex With N05859B
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, UBIQUITOUSLY-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, 16)

No.	Name	Count	Type	Full Name
1	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	MN	2	Ligand/Ion	MANGANESE (II) ION
2	MN1	2	Ligand/Ion	4-CARBOXYPIPERIDINE
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	MN1	1	Ligand/Ion	4-CARBOXYPIPERIDINE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	MN1	1	Ligand/Ion	4-CARBOXYPIPERIDINE
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (16, 16)

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 A2345
02	AC2	SOFTWARE	CYS B:1278 , CYS B:1281 , CYS B:1305 , CYS B:1308	BINDING SITE FOR RESIDUE ZN B2346
03	AC3	SOFTWARE	HIS B:1093 , GLU B:1095 , HIS B:1173 , HOH B:2152 , HOH B:2162 , MN1 B:2348	BINDING SITE FOR RESIDUE MN B2347
04	AC4	SOFTWARE	HIS A:1093 , GLU A:1095 , HIS A:1173 , HOH A:2176 , HOH A:2184 , MN1 A:2347	BINDING SITE FOR RESIDUE MN A2346
05	AC5	SOFTWARE	PHE B:1031 , LYS B:1084 , THR B:1090 , HIS B:1093 , ASN B:1103 , TRP B:1113 , HIS B:1173 , VAL B:1175 , HOH B:2146 , HOH B:2152 , HOH B:2162 , HOH B:2169 , MN B:2347	BINDING SITE FOR RESIDUE MN1 B2348
06	AC6	SOFTWARE	PHE A:1031 , LYS A:1084 , THR A:1090 , HIS A:1093 , ASN A:1103 , TRP A:1113 , HIS A:1173 , HOH A:2169 , HOH A:2176 , HOH A:2184 , MN A:2346	BINDING SITE FOR RESIDUE MN1 A2347
07	AC7	SOFTWARE	ILE B:967 , TRP B:968 , ARG B:969 , ASN B:1131 , HOH B:2353	BINDING SITE FOR RESIDUE EDO B2349
08	AC8	SOFTWARE	SER A:932 , THR A:933 , GLN A:986 , PRO A:1108 , ASN A:1182 , HOH A:2061 , EDO A:2349	BINDING SITE FOR RESIDUE EDO A2348
09	AC9	SOFTWARE	PHE A:990 , TRP A:1180 , HOH A:2099 , EDO A:2348	BINDING SITE FOR RESIDUE EDO A2349
10	BC1	SOFTWARE	ASN A:884 , PRO A:885 , ARG A:1156 , GLU B:999	BINDING SITE FOR RESIDUE EDO A2350
11	BC2	SOFTWARE	HIS A:1267 , HIS A:1276 , TYR A:1301 , VAL A:1303	BINDING SITE FOR RESIDUE EDO A2351
12	BC3	SOFTWARE	GLY A:919 , ALA A:921 , GLY A:922 , PRO A:1161 , GLY A:1162 , ASP A:1163 , HOH A:2049 , HOH A:2411 , HOH A:2412	BINDING SITE FOR RESIDUE EDO A2352
13	BC4	SOFTWARE	LYS A:895 , VAL B:1123 , ASP B:1126 , PHE B:1127 , HOH B:2354	BINDING SITE FOR RESIDUE EDO B2350
14	BC5	SOFTWARE	PRO A:910 , ASN A:912 , PRO A:913 , ASN A:1168 , ALA A:1169 , CYS A:1194 , LEU A:1198 , HOH A:2201	BINDING SITE FOR RESIDUE EDO A2353
15	BC6	SOFTWARE	GLN B:986 , PHE B:990 , PRO B:1108 , TRP B:1180 , HOH B:2090 , EDO B:2352 , HOH B:2355	BINDING SITE FOR RESIDUE EDO B2351
16	BC7	SOFTWARE	SER B:932 , THR B:933 , GLN B:986 , GLY B:1107 , ASN B:1182 , HOH B:2039 , EDO B:2351	BINDING SITE FOR RESIDUE EDO B2352

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

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 5FXV)

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

(no "Exon" information available for 5FXV)

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:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeeee....................eeeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhhhhhhhhh.....................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
                5fxv A  880 KDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLS 1344
                                   889       899       909       919       929       939       949       959       969       979       989       999|     1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342  
                                                                                                                                                 999|                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                 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.hhhhhhhhhhhhhh...eeeeeeee....................eeeeeeehhhhhhhhhhhhhhhhhhhh...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
                5fxv B  881 DKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSS 1345
                                   890       900       910       920       930       940       950       960       970       980       990      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336         
                                                                                                                                                999|                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                1026

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 5FXV)

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

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

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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 5fxw 5fxx 5fxz 5fy0 5fy1 5fy7 5fym

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

Description

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Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

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