4EZH - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF KDM6B BOUND WITH H3K27ME3 PEPTIDE

Authors :   Z. J. Cheng, D. J. Patel

Date :   02 May 12 (Deposition) - 08 Aug 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.52

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

Keywords :   Jmjc, Histone Demethylase, Histone K27Me3/Me2 'Eraser', Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Kruidenier, C. W. Chung, Z. Cheng, J. Liddle, K. Che, G. Joberty, M. Bantscheff, C. Bountra, A. Bridges, H. Diallo, D. Eberhard, S. Hutchinson, E. Jones, R. Katso, M. Leveridge, P. K. Mander, J. Mosley, C. Ramirez-Molina, P. Rowland, C. J. Schofield, R. J. Sheppard, J. E. Smith, C. Swales, R. Tanner, P. Thomas, A. Tumber, G. Drewes, U. Oppermann, D. J. Patel, K. Lee, D. M. Wilson
A Selective Jumonji H3K27 Demethylase Inhibitor Modulates The Proinflammatory Macrophage Response.
Nature V. 488 404 2012
PubMed-ID: 22842901 | Reference-DOI: 10.1038/NATURE11262

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 6B
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28 SUMO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1155-1641
	Gene	:	KDM6B, JMJD3, KIAA0346
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	JMJC DOMAIN-CONTAINING PROTEIN 3, JUMONJI DOMAIN-CONTAINING PROTEIN 3

Molecule 2 - SYNTHESIZED METHYLATION PEPTIDE
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	THIS SEQUENCE WAS SYNTHESIZED BY TUFTS UNIVERSITY
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:1390 , GLU A:1392 , HIS A:1470 , OGA A:1703 , HOH A:1813	BINDING SITE FOR RESIDUE NI A 1701
2	AC2	SOFTWARE	CYS A:1575 , CYS A:1578 , CYS A:1602 , CYS A:1605	BINDING SITE FOR RESIDUE ZN A 1702
3	AC3	SOFTWARE	LYS A:1381 , THR A:1387 , HIS A:1390 , GLU A:1392 , SER A:1398 , ASN A:1400 , HIS A:1470 , ALA A:1482 , NI A:1701 , HOH A:1801 , HOH A:1813 , M3L C:27	BINDING SITE FOR RESIDUE OGA A 1703
4	AC4	SOFTWARE	HIS B:1390 , GLU B:1392 , HIS B:1470 , OGA B:1703 , HOH B:1811	BINDING SITE FOR RESIDUE NI B 1701
5	AC5	SOFTWARE	CYS B:1575 , CYS B:1578 , CYS B:1602 , CYS B:1605	BINDING SITE FOR RESIDUE ZN B 1702
6	AC6	SOFTWARE	LYS B:1381 , THR B:1387 , HIS B:1390 , GLU B:1392 , SER B:1398 , ASN B:1400 , HIS B:1470 , NI B:1701 , HOH B:1802 , HOH B:1811 , M3L D:27	BINDING SITE FOR RESIDUE OGA B 1703

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

Asymmetric Unit

No.	Residues
1	Gly A:1404	-	Pro A:1405
2	Gly B:1404	-	Pro B:1405

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

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

(no "Exon" information available for 4EZH)

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:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh...........hhhhhh....eee....hhhhhhhhhhhhhh....eeeeehhhhhh..hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhh.........eeeeeeeeee.....hhhhhhhhhhhhhhhh.....hhhhhh.........eeeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........ee......ee..eeeee...eeehhhhhhh........eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ezh A 1157 ESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEELEVLFQHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296    ||1327      1337      1347      1357      1367      1377      1387      1397      1407      1417      1427      1437      1447      1457      1467      1477      1487      1497      1507      1517      1527      1537      1547      1557      1567      1577      1587  ||  1603      1613      1623      1633     
                                                                                                                                                                         1301|                                                                                                                                                                                                                                                                       1590|                                         
                                                                                                                                                                          1323                                                                                                                                                                                                                                                                        1597

Chain B from PDB  Type:PROTEIN  Length:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh........hhhhh.....eee....hhhhhhhhhhhhh.....eeeeehhhhhh..hhhhhhhhhhhhhh...eeeeeeee.....................eeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.....hhhhhhhhhhhhhhhh.....hhhhhh.........eeeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.........ee......ee..eeeee...eeehhhhhhh........eeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ezh B 1157 ESYLSPAQSVKPKIEKLPREKLNPPTPSIYLESKRDAFSPVLLQFCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGEHTVEVRTQVQQPSDENWDLTGTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEELEVLFHHIIKFGTNIDLSDAKRWKPQLQELLKLPAFMRVTSTGNMLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHGVDYLTGSWWPILDDLYASNIPVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNVGPLTAYQYQLALERYEWNEVKNVKSIVPMIHVSWNVARTVKISDPDLFKMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSTYLVHCEGCARRRSAGLQGVVVLEQYRTEELAQAYDAFTLAP 1638
                                  1166   || 1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299||    1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561      1571      1581      1597      1607      1617      1627      1637 
                                      1170|                                                                                                                          1300|                                                                                                                                                                                                                                                                       1590|                                         
                                       1174                                                                                                                           1323                                                                                                                                                                                                                                                                        1597

Chain C from PDB  Type:PROTEIN  Length:11
                                            
               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
                4ezh C   24 AARkSAPATGG   34
                               |    33 
                              27-M3L

Chain D from PDB  Type:PROTEIN  Length:11
                                            
               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
                4ezh D   24 AARkSAPATGG   34
                               |    33 
                              27-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 '\|'

(no "SCOP Domain" information available for 4EZH)

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

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

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	Ligands, Modified Residues, Ions
		M3L	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:1404 - Pro A:1405	[ RasMol ]
		Gly B:1404 - Pro B:1405	[ RasMol ]

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

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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