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Title :   JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27ME3 PEPTIDE (16-35)

Authors :   R. Chowdhury, D. Zafred, C. J. Schofield

Date :   15 Oct 14 (Deposition) - 26 Nov 14 (Release) - 11 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

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

Keywords :   Jmjd2A, Oxidoreductase, Non-Heme, Iron, 2-Oxoglutarate, Dioxygenase, Oxygenase, Double-Stranded Beta Helix, Dsbh, Facial Triad, Demethylase, Histone, Jmjc Domain, Metal Binding Protein, Epigenetic And Transcription Regulation, Chromatin Regulator, Hydroxylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. T. Williams, L. J. Walport, R. J. Hopkinson, S. K. Madden, R. Chowdhury, C. J. Schofield, A. Kawamura
Studies On The Catalytic Domains Of Multiple Jmjc Oxygenases Using Peptide Substrates.
Epigenetics V. 9 1596 2014
PubMed-ID: 25625844 | Reference-DOI: 10.4161/15592294.2014.983381

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 Variant	:	R3
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN 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

Molecule 2 - HISTONE H3.1T
	Chains	:	C
	Fragment	:	HISTONE H3K27ME3 PEPTIDE, RESIDUES 17-36
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 10)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
4	NI	2	Ligand/Ion	NICKEL (II) ION
5	OGA	2	Ligand/Ion	N-OXALYLGLYCINE
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
4	NI	-1	Ligand/Ion	NICKEL (II) ION
5	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	M3L	-1	Mod. Amino Acid	N-TRIMETHYLLYSINE
4	NI	-1	Ligand/Ion	NICKEL (II) ION
5	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:188 , GLU A:190 , HIS A:276 , OGA A:601 , HOH A:2152	BINDING SITE FOR RESIDUE NI A 501
2	AC2	SOFTWARE	CYS A:234 , HIS A:240 , CYS A:306 , CYS A:308	BINDING SITE FOR RESIDUE ZN A 502
3	AC3	SOFTWARE	PHE A:227 , GLY A:229 , SER A:230	BINDING SITE FOR RESIDUE CL A 503
4	AC4	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 , NI A:501 , HOH A:2253	BINDING SITE FOR RESIDUE OGA A 601
5	AC5	SOFTWARE	TYR A:59 , ASP A:60 , ARG A:98 , PHE A:283 , HOH A:2045 , HOH A:2093	BINDING SITE FOR RESIDUE GOL A 702
6	AC6	SOFTWARE	HIS B:188 , GLU B:190 , HIS B:276 , OGA B:601 , HOH B:2137	BINDING SITE FOR RESIDUE NI B 501
7	AC7	SOFTWARE	CYS B:234 , HIS B:240 , CYS B:306 , CYS B:308	BINDING SITE FOR RESIDUE ZN B 502
8	AC8	SOFTWARE	PHE B:227 , GLY B:229	BINDING SITE FOR RESIDUE CL B 503
9	AC9	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 , NI B:501 , HOH B:2136 , HOH B:2247	BINDING SITE FOR RESIDUE OGA B 601

(no "SS Bond" information available for 4V2W)

(no "Cis Peptide Bond" information available for 4V2W)

(no "SAP(SNP)/Variant" information available for 4V2W)

(no "PROSITE Motif" information available for 4V2W)

(no "Exon" information available for 4V2W)

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
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Chain A from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhh...........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhh.............hhhhhhhhhhhhhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4v2w A   7 TLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL 354
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346

Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee.............hhhh.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
                 4v2w B   3 SESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLK 355
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain C from PDB  Type:PROTEIN  Length:4
                                    
               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
                 4v2w C  25 ARkS  28
                              | 
                             27-M3L

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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 4V2W)

(no "CATH Domain" information available for 4V2W)

(no "Pfam Domain" information available for 4V2W)

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4v2v	JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27ME3 PEPTIDE (25-29) ARK(ME3)SA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 10)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (37, 40)

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