2P5B - JenaLib

Asym.Unit - manually (Jmol Viewer)

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 :   THE COMPLEX STRUCTURE OF JMJD2A AND TRIMETHYLATED H3K36 PEPTIDE

Authors :   G. Zhang, Z. Chen, J. Zang, X. Hong, Y. Shi

Date :   14 Mar 07 (Deposition) - 12 Jun 07 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.99

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

Keywords :   Jmjd2A, Jmjc Domain, Histone Demethylase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Chen, J. Zang, J. Kappler, X. Hong, F. Crawford, Q. Wang, F. Lan, C. Jiang, J. Whetstine, S. Dai, K. Hansen, Y. Shi, G. Zhang
Structural Basis Of The Recognition Of A Methylated Histone Tail By Jmjd2A.
Proc. Natl. Acad. Sci. Usa V. 104 10818 2007
PubMed-ID: 17567753 | Reference-DOI: 10.1073/PNAS.0704525104

Molecule 1 - JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX 4T2
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC CORE
	Gene	:	JMJD2A, JHDM3A, JMJD2, KIAA0677
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JUMONJI DOMAIN-CONTAINING PROTEIN 2A

Molecule 2 - HISTONE H3
	Chains	:	I, J
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	I	J
Biological Unit 1 (1x)	:	A		I
Biological Unit 2 (1x)	:		B		J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	FE2	2	Ligand/Ion	FE (II) ION
2	M3L	2	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	OGA	2	Ligand/Ion	N-OXALYLGLYCINE
4	OXY	3	Ligand/Ion	OXYGEN MOLECULE
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION
2	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
4	OXY	2	Ligand/Ion	OXYGEN MOLECULE
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION
2	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
3	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
4	OXY	1	Ligand/Ion	OXYGEN MOLECULE
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308	BINDING SITE FOR RESIDUE ZN A 351
2	AC2	SOFTWARE	CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308	BINDING SITE FOR RESIDUE ZN B 351
3	AC3	SOFTWARE	HIS A:188 , GLU A:190 , HIS A:276 , OGA A:401 , OXY A:502	BINDING SITE FOR RESIDUE FE2 A 352
4	AC4	SOFTWARE	HIS B:188 , GLU B:190 , HIS B:276 , OGA B:402 , OXY B:503	BINDING SITE FOR RESIDUE FE2 B 352
5	AC5	SOFTWARE	TYR A:132 , PHE A:185 , HIS A:188 , GLU A:190 , SER A:196 , ASN A:198 , LYS A:206 , TRP A:208 , HIS A:276 , FE2 A:352 , OXY A:502	BINDING SITE FOR RESIDUE OGA A 401
6	AC6	SOFTWARE	TYR B:132 , PHE B:185 , HIS B:188 , GLU B:190 , SER B:196 , ASN B:198 , LYS B:206 , TRP B:208 , HIS B:276 , FE2 B:352 , OXY B:503 , HOH B:604	BINDING SITE FOR RESIDUE OGA B 402
7	AC7	SOFTWARE	HIS A:188 , GLU A:190 , ASP A:191 , LYS A:241 , OXY A:502 , HOH A:578 , M3L I:10	BINDING SITE FOR RESIDUE OXY A 501
8	AC8	SOFTWARE	HIS A:188 , GLU A:190 , LYS A:241 , FE2 A:352 , OGA A:401 , OXY A:501 , M3L I:10	BINDING SITE FOR RESIDUE OXY A 502
9	AC9	SOFTWARE	HIS B:188 , GLU B:190 , LYS B:241 , FE2 B:352 , OGA B:402 , HOH B:593 , M3L J:10	BINDING SITE FOR RESIDUE OXY B 503

(no "SS Bond" information available for 2P5B)

(no "Cis Peptide Bond" information available for 2P5B)

(no "SAP(SNP)/Variant" information available for 2P5B)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJN	PS51183	JmjN domain profile.	KDM4A_HUMAN	14-56	2	A:14-56 B:14-56
2	JMJC	PS51184	JmjC domain profile.	KDM4A_HUMAN	142-308	2	A:142-308 B:142-308

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJN	PS51183	JmjN domain profile.	KDM4A_HUMAN	14-56	1	A:14-56 -
2	JMJC	PS51184	JmjC domain profile.	KDM4A_HUMAN	142-308	1	A:142-308 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJN	PS51183	JmjN domain profile.	KDM4A_HUMAN	14-56	1	- B:14-56
2	JMJC	PS51184	JmjC domain profile.	KDM4A_HUMAN	142-308	1	- B:142-308

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000372396	1b	ENSE00001894244	chr1:44115829-44115923	95	KDM4A_HUMAN	-	0	0	-	-
1.3a	ENST00000372396	3a	ENSE00002186574	chr1:44118808-44118984	177	KDM4A_HUMAN	1-46	46	2	A:2-46 B:10-46	45 37
1.5	ENST00000372396	5	ENSE00001143140	chr1:44121262-44121437	176	KDM4A_HUMAN	47-105	59	2	A:47-105 B:47-105	59 59
1.6	ENST00000372396	6	ENSE00000957378	chr1:44125969-44126083	115	KDM4A_HUMAN	105-143	39	2	A:105-143 B:105-143	39 39
1.7	ENST00000372396	7	ENSE00000957379	chr1:44128565-44128758	194	KDM4A_HUMAN	144-208	65	2	A:144-208 B:144-208	65 65
1.8	ENST00000372396	8	ENSE00000957380	chr1:44131367-44131416	50	KDM4A_HUMAN	208-225	18	2	A:208-225 B:208-225	18 18
1.9b	ENST00000372396	9b	ENSE00001690958	chr1:44132123-44132226	104	KDM4A_HUMAN	225-259	35	2	A:225-259 B:225-259	35 35
1.10c	ENST00000372396	10c	ENSE00000957382	chr1:44132625-44132762	138	KDM4A_HUMAN	260-305	46	2	A:260-305 B:260-305	46 46
1.11	ENST00000372396	11	ENSE00000957383	chr1:44133443-44133690	248	KDM4A_HUMAN	306-388	83	2	A:306-348 B:306-346	43 41
1.12	ENST00000372396	12	ENSE00000957384	chr1:44134771-44134970	200	KDM4A_HUMAN	388-455	68	0	-	-
1.13b	ENST00000372396	13b	ENSE00000957385	chr1:44137176-44137546	371	KDM4A_HUMAN	455-578	124	0	-	-
1.14	ENST00000372396	14	ENSE00001080538	chr1:44149355-44149475	121	KDM4A_HUMAN	579-619	41	0	-	-
1.15	ENST00000372396	15	ENSE00000957387	chr1:44154585-44154766	182	KDM4A_HUMAN	619-679	61	0	-	-
1.16b	ENST00000372396	16b	ENSE00001143055	chr1:44156516-44156720	205	KDM4A_HUMAN	680-748	69	0	-	-
1.17	ENST00000372396	17	ENSE00001143047	chr1:44157167-44157243	77	KDM4A_HUMAN	748-773	26	0	-	-
1.18b	ENST00000372396	18b	ENSE00001143039	chr1:44157927-44157982	56	KDM4A_HUMAN	774-792	19	0	-	-
1.19	ENST00000372396	19	ENSE00001143030	chr1:44159665-44159773	109	KDM4A_HUMAN	792-828	37	0	-	-
1.20	ENST00000372396	20	ENSE00001143023	chr1:44160380-44160565	186	KDM4A_HUMAN	829-890	62	0	-	-
1.21	ENST00000372396	21	ENSE00001080535	chr1:44163514-44163684	171	KDM4A_HUMAN	891-947	57	0	-	-
1.22a	ENST00000372396	22a	ENSE00001080539	chr1:44169288-44169407	120	KDM4A_HUMAN	948-987	40	0	-	-
1.23	ENST00000372396	23	ENSE00001080536	chr1:44169691-44169783	93	KDM4A_HUMAN	988-1018	31	0	-	-
1.24a	ENST00000372396	24a	ENSE00001841454	chr1:44169901-44171186	1286	KDM4A_HUMAN	1019-1064	46	0	-	-

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:347
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:347
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
          KDM4A_HUMAN     2 ASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTP 348
               SCOP domains d2p5ba_ A: JMJD2A core                                                                                                                                                                                                                                                                                                                                      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.............hhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------JMJN  PDB: A:14-56 UniProt: 14-56          -------------------------------------------------------------------------------------JMJC  PDB: A:142-308 UniProt: 142-308                                                                                                                                  ---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:2-46 UniProt: 1-46         Exon 1.5  PDB: A:47-105 UniProt: 47-105                    --------------------------------------Exon 1.7  PDB: A:144-208 UniProt: 144-208                        ----------------Exon 1.9b  PDB: A:225-259          Exon 1.10c  PDB: A:260-305 UniProt: 260-305   Exon 1.11  PDB: A:306-348 UniProt: 306-388  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:105-143               ----------------------------------------------------------------Exon 1.8          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2p5b A   2 ASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTP 348
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with KDM4A_HUMAN | O75164 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:337
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       
          KDM4A_HUMAN    10 PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLP 346
               SCOP domains d2p5bb_ B: JMJD2A core                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----JmjN-2p5bB03 B:15-49               -----------------------------------------------------------------------------------------------------------------------------JmjC-2p5bB01 B:175-291                                                                                               ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----JmjN-2p5bB04 B:15-49               -----------------------------------------------------------------------------------------------------------------------------JmjC-2p5bB02 B:175-291                                                                                               ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----JMJN  PDB: B:14-56 UniProt: 14-56          -------------------------------------------------------------------------------------JMJC  PDB: B:142-308 UniProt: 142-308                                                                                                                                  -------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: B:10-46 UniProt: 1-46Exon 1.5  PDB: B:47-105 UniProt: 47-105                    --------------------------------------Exon 1.7  PDB: B:144-208 UniProt: 144-208                        ----------------Exon 1.9b  PDB: B:225-259          Exon 1.10c  PDB: B:260-305 UniProt: 260-305   Exon 1.11  PDB: B:306-346 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.6  PDB: B:105-143               ----------------------------------------------------------------Exon 1.8          ------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2p5b B  10 PSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLP 346
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

Chain I from PDB  Type:PROTEIN  Length:17
 aligned with H3_URECA | P84239 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:17
                                    37       
             H3_URECA    28 KSAPATGGVKKPHRYRP  44
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ................. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 2p5b I   1 KSAPATGGVkKPHRYRP  17
                                    10       
                                    10-M3L

Chain J from PDB  Type:PROTEIN  Length:14
 aligned with H3_URECA | P84239 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:14
                                    37    
             H3_URECA    28 KSAPATGGVKKPHR  41
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 2p5b J   1 KSAPATGGVkKPHR  14
                                    10    
                                    10-M3L

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: Histone demethylase core (19)

Protein domain: JMJD2A core (13)

Human (Homo sapiens) [TaxId: 9606] (13)

1a	d2p5ba_	A:
1b	d2p5bb_	B:

(no "CATH Domain" information available for 2P5B)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: JmjC (39)

Homo sapiens (Human) (31)

1a	JmjC-2p5bB01	B:175-291
1b	JmjC-2p5bB02	B:175-291

Clan: no clan defined [family: JmjN] (16)

Family: JmjN (16)

Homo sapiens (Human) (16)

2a	JmjN-2p5bB03	B:15-49
2b	JmjN-2p5bB04	B:15-49

Asymmetric Unit(hide GO term definitions)

Chain A,B (KDM4A_HUMAN | O75164)

molecular function
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0032452	histone demethylase activity	Catalysis of the removal of a methyl group from a histone.
	GO:0051864	histone demethylase activity (H3-K36 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0014898	cardiac muscle hypertrophy in response to stress	The physiological enlargement or overgrowth of all or part of the heart muscle due to an increase in size (not length) of individual cardiac muscle fibers, without cell division, as a result of a disturbance in organismal or cellular homeostasis.
	GO:0070544	histone H3-K36 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
	GO:0016577	histone demethylation	The modification of histones by removal of methyl groups.
	GO:0010507	negative regulation of autophagy	Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1900113	negative regulation of histone H3-K9 trimethylation	Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K9 trimethylation.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005721	pericentric heterochromatin	Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.

Chain I,J (H3_URECA | P84239)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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
		FE2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		M3L	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		OGA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		OXY	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2p5b)

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
	2p5b
		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
	H3_URECA \| P84239
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	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
	H3_URECA \| P84239
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	KDM4A_HUMAN \| O75164
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2gp3	THE STRUCTURE OF CATALYTIC CORE OF JMJD2A
2gp5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (8, 16)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (29, 30)

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