5A7O - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 42

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, D. M. Pinkas, F. Von Delft, C. H. Arrowsmith, C. Boun A. Edwards, B. K. Shoichet, D. G. Fujimori, U. Oppermann

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

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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, 26)

No.	Name	Count	Type	Full Name
1	7WH	2	Ligand/Ion	2-[5-(2-METHOXYETHANOYLAMINO)-2-OXIDANYL-PHENYL]PYRIDINE-4-CARBOXYLIC ACID
2	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	16	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, 14)

No.	Name	Count	Type	Full Name
1	7WH	1	Ligand/Ion	2-[5-(2-METHOXYETHANOYLAMINO)-2-OXIDANYL-PHENYL]PYRIDINE-4-CARBOXYLIC ACID
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	11	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, 8)

No.	Name	Count	Type	Full Name
1	7WH	1	Ligand/Ion	2-[5-(2-METHOXYETHANOYLAMINO)-2-OXIDANYL-PHENYL]PYRIDINE-4-CARBOXYLIC ACID
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	EDO	5	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 (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:227 , PRO A:228 , GLY A:229 , SER A:230 , HOH A:2108 , HOH A:2109 , LYS B:105	BINDING SITE FOR RESIDUE SO4 A1355
02	AC2	SOFTWARE	LYS A:105 , PHE B:227 , PRO B:228 , GLY B:229 , SER B:230	BINDING SITE FOR RESIDUE SO4 B1355
03	AC3	SOFTWARE	TYR A:132 , PHE A:185 , HIS A:188 , GLU A:190 , ASN A:198 , LYS A:206 , TRP A:208 , LYS A:241 , HIS A:276 , MN A:1369 , DMS A:1370 , HOH A:2030 , HOH A:2086	BINDING SITE FOR RESIDUE 7WH A1356
04	AC4	SOFTWARE	TYR B:132 , TYR B:177 , PHE B:185 , HIS B:188 , GLU B:190 , LYS B:206 , TRP B:208 , LYS B:241 , HIS B:276 , MN B:1363 , DMS B:1364 , HOH B:2066 , HOH B:2085	BINDING SITE FOR RESIDUE 7WH B1356
05	AC5	SOFTWARE	SER A:316 , MET A:317 , ASP A:318 , HOH A:2152 , HOH A:2172	BINDING SITE FOR RESIDUE EDO A1357
06	AC6	SOFTWARE	LYS A:224 , GLU A:235 , ALA A:236 , PHE A:237 , LEU A:238 , EDO A:1367 , HOH A:2112	BINDING SITE FOR RESIDUE EDO A1358
07	AC7	SOFTWARE	LYS B:224 , GLU B:235 , ALA B:236 , PHE B:237 , LEU B:238 , HOH B:2103 , HOH B:2116	BINDING SITE FOR RESIDUE EDO B1357
08	AC8	SOFTWARE	GLN B:73 , LEU B:74 , VAL B:75 , LEU B:125 , THR B:126 , PHE B:127 , PRO B:129 , PRO B:130	BINDING SITE FOR RESIDUE EDO B1358
09	AC9	SOFTWARE	ARG A:98	BINDING SITE FOR RESIDUE EDO A1359
10	BC1	SOFTWARE	LEU A:81 , PHE A:82 , THR A:83 , PHE A:227 , HOH B:2061	BINDING SITE FOR RESIDUE EDO A1360
11	BC2	SOFTWARE	LYS A:217 , TYR A:273 , GLN A:302 , VAL A:304 , HOH A:2089	BINDING SITE FOR RESIDUE EDO A1361
12	BC3	SOFTWARE	GLN A:78 , SER A:79 , TRP A:122 , LYS A:123 , HOH A:2027 , HOH A:2050	BINDING SITE FOR RESIDUE EDO A1362
13	BC4	SOFTWARE	ARG B:25 , PHE B:27 , ASP B:146 , TRP B:148 , ASN B:149	BINDING SITE FOR RESIDUE EDO B1359
14	BC5	SOFTWARE	GLY A:138 , THR A:139	BINDING SITE FOR RESIDUE EDO A1363
15	BC6	SOFTWARE	GLU A:23 , ARG A:29 , HOH A:2010	BINDING SITE FOR RESIDUE EDO A1364
16	BC7	SOFTWARE	LYS B:217 , GLN B:302 , HOH B:2088	BINDING SITE FOR RESIDUE EDO B1360
17	BC8	SOFTWARE	MET A:312 , VAL A:313 , LYS A:314	BINDING SITE FOR RESIDUE EDO A1365
18	BC9	SOFTWARE	LYS A:89 , LYS A:90	BINDING SITE FOR RESIDUE EDO A1366
19	CC1	SOFTWARE	HIS A:188 , THR A:189 , LEU A:238 , ARG A:239 , TYR A:275 , EDO A:1358	BINDING SITE FOR RESIDUE EDO A1367
20	CC2	SOFTWARE	ARG B:98	BINDING SITE FOR RESIDUE EDO B1361
21	CC3	SOFTWARE	CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308	BINDING SITE FOR RESIDUE ZN A1368
22	CC4	SOFTWARE	CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308	BINDING SITE FOR RESIDUE ZN B1362
23	CC5	SOFTWARE	HIS A:188 , GLU A:190 , HIS A:276 , 7WH A:1356 , HOH A:2086	BINDING SITE FOR RESIDUE MN A1369
24	CC6	SOFTWARE	HIS B:188 , GLU B:190 , HIS B:276 , 7WH B:1356 , HOH B:2085	BINDING SITE FOR RESIDUE MN B1363
25	CC7	SOFTWARE	GLY A:170 , TYR A:177 , GLU A:190 , SER A:288 , 7WH A:1356	BINDING SITE FOR RESIDUE DMS A1370
26	CC8	SOFTWARE	GLY B:170 , TYR B:175 , TYR B:177 , GLU B:190 , SER B:288 , ASN B:290 , 7WH B:1356	BINDING SITE FOR RESIDUE DMS B1364

(no "SS Bond" information available for 5A7O)

(no "Cis Peptide Bond" information available for 5A7O)

(no "SAP(SNP)/Variant" information available for 5A7O)

(no "PROSITE Motif" information available for 5A7O)

(no "Exon" information available for 5A7O)

Asymmetric Unit

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Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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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 hhhhh......eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a7o A   4 ESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFE 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 .hhhhh.eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhh...........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhh..hhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a7o B   8 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFE 354
                                    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

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5A7O)

(no "CATH Domain" information available for 5A7O)

(no "Pfam Domain" information available for 5A7O)

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	5a7o
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5a7n	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 43
5a7p	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 36
5a7q	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 30
5a7s	CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 44

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 26)

Sites (26, 26)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (25, 25)

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