5FXW - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

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

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) - 14 Jun 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 :   Transferase, 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 Fumarate
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, 21)

No.	Name	Count	Type	Full Name
1	EDO	15	Ligand/Ion	1,2-ETHANEDIOL
2	FUM	2	Ligand/Ion	FUMARIC 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	FUM	1	Ligand/Ion	FUMARIC 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	FUM	1	Ligand/Ion	FUMARIC 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 A 1401
02	AC2	SOFTWARE	HIS A:1093 , GLU A:1095 , HIS A:1173 , FUM A:1403 , EDO A:1410 , HOH A:1501 , HOH A:1518	binding site for residue MN A 1402
03	AC3	SOFTWARE	LYS A:1084 , THR A:1090 , HIS A:1093 , ASN A:1103 , HIS A:1173 , ASN A:1183 , MN A:1402 , HOH A:1501 , HOH A:1518 , HOH A:1666	binding site for residue FUM A 1403
04	AC4	SOFTWARE	SER A:932 , THR A:933 , GLN A:986 , PRO A:1108 , ASN A:1182 , EDO A:1405 , EDO A:1409 , HOH A:1689	binding site for residue EDO A 1404
05	AC5	SOFTWARE	TRP A:1180 , EDO A:1404 , HOH A:1510	binding site for residue EDO A 1405
06	AC6	SOFTWARE	ARG A:1156 , GLU B:999	binding site for residue EDO A 1406
07	AC7	SOFTWARE	HIS A:1267 , GLU A:1273 , HIS A:1276 , TYR A:1301 , VAL A:1303	binding site for residue EDO A 1407
08	AC8	SOFTWARE	GLY A:919 , ALA A:921 , GLY A:922 , PRO A:1161 , GLY A:1162 , ASP A:1163 , HOH A:1507 , HOH A:1670	binding site for residue EDO A 1408
09	AC9	SOFTWARE	LEU A:928 , GLY A:929 , SER A:932 , EDO A:1404	binding site for residue EDO A 1409
10	AD1	SOFTWARE	GLY A:1075 , GLN A:1080 , TYR A:1082 , GLU A:1095 , SER A:1101 , TRP A:1186 , ASN A:1187 , MN A:1402 , HOH A:1501	binding site for residue EDO A 1410
11	AD2	SOFTWARE	CYS B:1278 , CYS B:1281 , CYS B:1305 , CYS B:1308	binding site for residue ZN B 1401
12	AD3	SOFTWARE	HIS B:1093 , GLU B:1095 , HIS B:1173 , FUM B:1403 , HOH B:1511 , HOH B:1535	binding site for residue MN B 1402
13	AD4	SOFTWARE	LYS B:1084 , THR B:1090 , HIS B:1093 , ASN B:1103 , HIS B:1173 , ASN B:1183 , MN B:1402 , HOH B:1511 , HOH B:1535 , HOH B:1677	binding site for residue FUM B 1403
14	AD5	SOFTWARE	ILE B:967 , TRP B:968 , ARG B:969 , ASN B:1131 , LEU B:1133 , HOH B:1706	binding site for residue EDO B 1404
15	AD6	SOFTWARE	LYS A:895 , VAL B:1123 , ASP B:1126 , PHE B:1127 , HOH B:1650	binding site for residue EDO B 1405
16	AD7	SOFTWARE	PHE B:990 , PRO B:1108 , TRP B:1180 , EDO B:1407 , HOH B:1525	binding site for residue EDO B 1406
17	AD8	SOFTWARE	SER B:932 , THR B:933 , GLN B:986 , ASN B:1182 , EDO B:1406 , HOH B:1716	binding site for residue EDO B 1407
18	AD9	SOFTWARE	LEU B:1050 , THR B:1051 , ARG B:1058 , VAL B:1059 , VAL B:1060 , HOH B:1621	binding site for residue EDO B 1408
19	AE1	SOFTWARE	ASP B:1036 , ASP B:1039 , LYS B:1042 , HOH B:1566 , HOH B:1607	binding site for residue EDO B 1409
20	AE2	SOFTWARE	LYS B:1207 , SER B:1210 , CYS B:1281 , HOH B:1612	binding site for residue EDO B 1410
21	AE3	SOFTWARE	GLY B:1075 , GLN B:1080 , TYR B:1082 , GLU B:1095 , SER B:1101 , ALA B:1185 , TRP B:1186 , ASN B:1187 , HOH B:1511 , HOH B:1572 , HOH B:1601	binding site for residue EDO B 1411

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

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 5FXW)

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

(no "Exon" information available for 5FXW)

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:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh....eee..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhhhh..eeeeeeee....................eeeeeeehhhhhhhhhhhhhhhhhhhh........eeeeeeeee......hhhhhhhhhhhhhhhh.....hhhhhh..........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
                5fxw 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.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
                5fxw 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

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ 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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		AD1	[ RasMol ]	+environment [ RasMol ]
		AD2	[ RasMol ]	+environment [ RasMol ]
		AD3	[ RasMol ]	+environment [ RasMol ]
		AD4	[ RasMol ]	+environment [ RasMol ]
		AD5	[ RasMol ]	+environment [ RasMol ]
		AD6	[ RasMol ]	+environment [ RasMol ]
		AD7	[ RasMol ]	+environment [ RasMol ]
		AD8	[ RasMol ]	+environment [ RasMol ]
		AD9	[ RasMol ]	+environment [ RasMol ]
		AE1	[ RasMol ]	+environment [ RasMol ]
		AE2	[ RasMol ]	+environment [ RasMol ]
		AE3	[ RasMol ]	+environment [ RasMol ]

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

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	5fxw
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	UTY_HUMAN \| O14607
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	UTY_HUMAN \| O14607
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	UTY_HUMAN \| O14607	:	3zli 3zpo 4uf0 5a1l 5fxv 5fxx 5fxz 5fy0 5fy1 5fy7 5fym

5fxv	CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY IN COMPLEX WITH N05859B
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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File