5A7P - 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 HUMAN JMJD2A IN COMPLEX WITH COMPOUND 36

Authors :   R. Nowak, S. Velupillai, T. Krojer, C. Gileadi, C. Johansson, M. Korczy D. D. Le, N. Younger, E. Gregori-Puigjane, A. Tumber, E. Iwasa, S. B. Po I. Ortiz Torres, J. Kopec, C. Tallant, S. Froese, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, B. K. Shoichet, D. G. Fujimor U. Oppermann

Date :   09 Jul 15 (Deposition) - 13 Jan 16 (Release) - 09 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

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

Reference :   M. Korczynska, D. D. Le, N. Younger, E. Gregori-Puigjane, A. Tumber, T. Krojer, S. Velupillai, C. Gileadi, R. P. Nowak, E. Iwasa, S. B. Pollock, I. Ortiz Torres, U. Oppermann, B. K. Shoichet, D. G. Fujimori
Docking And Linking Of Fragments To Discover Jumonji Histone Demethylase Inhibitors.
J. Med. Chem. V. 59 1580 2016
PubMed-ID: 26699912 | Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01527

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	:	UNP RESIDUES 1-359
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, JUMONJI 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 (6, 18)

No.	Name	Count	Type	Full Name
1	6Z1	2	Ligand/Ion	2-[5-[(5-METHYL-1,2-OXAZOL-3-YL)CARBONYLAMINO]-2-OXIDANYL-PHENYL]PYRIDINE-4-CARBOXYLIC
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
4	MN	2	Ligand/Ion	MANGANESE (II) ION
5	SO4	2	Ligand/Ion	SULFATE ION
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	6Z1	1	Ligand/Ion	2-[5-[(5-METHYL-1,2-OXAZOL-3-YL)CARBONYLAMINO]-2-OXIDANYL-PHENYL]PYRIDINE-4-CARBOXYLIC
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	SO4	1	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	6Z1	1	Ligand/Ion	2-[5-[(5-METHYL-1,2-OXAZOL-3-YL)CARBONYLAMINO]-2-OXIDANYL-PHENYL]PYRIDINE-4-CARBOXYLIC
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	SO4	1	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:227 , PRO A:228 , GLY A:229 , SER A:230 , HOH A:2129 , HOH A:2185 , LYS B:105	BINDING SITE FOR RESIDUE SO4 A1354
02	AC2	SOFTWARE	LYS A:105 , PHE B:227 , PRO B:228 , GLY B:229 , SER B:230	BINDING SITE FOR RESIDUE SO4 B1354
03	AC3	SOFTWARE	HIS A:188 , GLU A:190 , HIS A:276 , 6Z1 A:1361 , HOH A:2103	BINDING SITE FOR RESIDUE MN A1355
04	AC4	SOFTWARE	HIS B:188 , GLU B:190 , HIS B:276 , 6Z1 B:1361 , HOH B:2102	BINDING SITE FOR RESIDUE MN B1355
05	AC5	SOFTWARE	CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308	BINDING SITE FOR RESIDUE ZN A1356
06	AC6	SOFTWARE	CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308	BINDING SITE FOR RESIDUE ZN B1356
07	AC7	SOFTWARE	LYS A:224 , GLU A:235 , ALA A:236 , PHE A:237 , LEU A:238 , EDO A:1358	BINDING SITE FOR RESIDUE EDO A1357
08	AC8	SOFTWARE	HIS A:188 , THR A:189 , LEU A:238 , ARG A:239 , TYR A:275 , EDO A:1357	BINDING SITE FOR RESIDUE EDO A1358
09	AC9	SOFTWARE	THR A:76 , LEU A:81 , PHE A:82 , THR A:83 , PHE A:227 , HOH A:2037	BINDING SITE FOR RESIDUE EDO A1359
10	BC1	SOFTWARE	THR B:76 , LEU B:81 , PHE B:82 , THR B:83 , PHE B:227 , HOH B:2045	BINDING SITE FOR RESIDUE EDO B1357
11	BC2	SOFTWARE	GLU B:235 , ALA B:236 , PHE B:237 , LEU B:238 , HOH B:2120	BINDING SITE FOR RESIDUE EDO B1358
12	BC3	SOFTWARE	GLY B:225	BINDING SITE FOR RESIDUE EDO B1359
13	BC4	SOFTWARE	TYR A:253 , GLY A:254 , HOH A:2123 , HOH A:2140 , HOH A:2187 , THR B:16 , LYS B:259 , VAL B:260	BINDING SITE FOR RESIDUE EDO A1360
14	BC5	SOFTWARE	ARG A:98 , LYS B:99 , ASN B:102	BINDING SITE FOR RESIDUE EDO B1360
15	BC6	SOFTWARE	ASN A:86 , TYR A:132 , PHE A:185 , HIS A:188 , GLU A:190 , LYS A:206 , TRP A:208 , LYS A:241 , HIS A:276 , MN A:1355 , DMS A:1362 , HOH A:2071 , HOH A:2103 , HOH A:2110 , HOH A:2136	BINDING SITE FOR RESIDUE 6Z1 A1361
16	BC7	SOFTWARE	ASN B:86 , TYR B:132 , PHE B:185 , HIS B:188 , GLU B:190 , LYS B:206 , TRP B:208 , LYS B:241 , HIS B:276 , MN B:1355 , DMS B:1362 , HOH B:2085 , HOH B:2102 , HOH B:2107 , HOH B:2162	BINDING SITE FOR RESIDUE 6Z1 B1361
17	BC8	SOFTWARE	GLY A:170 , TYR A:177 , SER A:288 , THR A:289 , 6Z1 A:1361 , HOH A:2110	BINDING SITE FOR RESIDUE DMS A1362
18	BC9	SOFTWARE	GLY B:170 , TYR B:177 , SER B:288 , THR B:289 , ASN B:290 , 6Z1 B:1361	BINDING SITE FOR RESIDUE DMS B1362

(no "SS Bond" information available for 5A7P)

(no "Cis Peptide Bond" information available for 5A7P)

(no "SAP(SNP)/Variant" information available for 5A7P)

(no "PROSITE Motif" information available for 5A7P)

(no "Exon" information available for 5A7P)

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:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................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
                 5a7p A   4 ESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhh.............eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhhhhhhhhhhh............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a7p B   8 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF 353
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347

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 5A7P)

(no "CATH Domain" information available for 5A7P)

(no "Pfam Domain" information available for 5A7P)

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
		6Z1	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a7p)

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
	5a7p
		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
	KDM4A_HUMAN \| O75164
		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)
	1.14.11.-
		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
	KDM4A_HUMAN \| O75164
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

5a7n	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 43
5a7o	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 42
5a7q	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 30
5a7s	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 44
5a7w	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 35
5a80	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 40

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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 (25, 25)

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