4J8V - JenaLib

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Title :   X-RAY STRUCTURE OF NCP145 WITH BOUND CHLORIDO(ETA-6-P-CYMENE)(N-PHENYL-2-PYRIDINECARBOTHIOAMIDE)RUTHENIUM(II)

Authors :   Z. Adhireksan, C. A. Davey

Date :   15 Feb 13 (Deposition) - 08 May 13 (Release) - 08 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.58

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,J  (1x)
Biol. Unit 2: E,F,G,H,I  (1x)
Biol. Unit 3: A,B,C,D,E,F,G,H,I,J  (1x)

Keywords :   Nucleosome, Histone, Structural Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Meier, M. Hanif, Z. Adhireksan, V. Pichler, M. Novak, E. Jirkovsky, M. A. Jakupec, V. B. Arion, C. A. Davey, B. K. Keppler, C. G. Hartinger
Novel Metal(Ii) Arene 2-Pyridinecarbothioamides: A Rational To Orally Active Organometallic Anticancer Agents
Chem Sci V. 4 1837 2013
PubMed: search | Reference-DOI: 10.1039/C3SC22294B

Molecule 1 - HISTONE H3.2
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	CLAWED FROG,COMMON PLATANNA,PLATANNA
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

Molecule 2 - HISTONE H4
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	CLAWED FROG,COMMON PLATANNA,PLATANNA
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

Molecule 3 - HISTONE H2A
	Chains	:	C, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HIST1H2AJ, LOC494591
	Organism Common	:	CLAWED FROG,COMMON PLATANNA,PLATANNA
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355

Molecule 4 - HISTONE H2B 1.1
	Chains	:	D, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	CLAWED FROG,COMMON PLATANNA,PLATANNA
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	H2B1.1

Molecule 5 - DNA (145-MER)
	Chains	:	I
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Molecule 6 - DNA (145-MER)
	Chains	:	J
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J
Biological Unit 1 (1x)	:	A	B	C	D						J
Biological Unit 2 (1x)	:					E	F	G	H	I
Biological Unit 3 (1x)	:	A	B	C	D	E	F	G	H	I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	RU7	2	Ligand/Ion	PARA-CYMENE RUTHENIUM CHLORIDE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	RU7	1	Ligand/Ion	PARA-CYMENE RUTHENIUM CHLORIDE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	RU7	1	Ligand/Ion	PARA-CYMENE RUTHENIUM CHLORIDE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	RU7	2	Ligand/Ion	PARA-CYMENE RUTHENIUM CHLORIDE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY C:44 , ALA C:45 , GLY C:46 , ALA C:47 , THR D:87 , SER D:88	BINDING SITE FOR RESIDUE SO4 D 1101
2	AC2	SOFTWARE	HIS D:79 , LEU G:33 , TYR G:39 , PHE H:67 , GLU H:68	BINDING SITE FOR RESIDUE RU7 D 1102
3	AC3	SOFTWARE	VAL D:45 , ASP E:77	BINDING SITE FOR RESIDUE MG E 1001
4	AC4	SOFTWARE	GLY G:44 , ALA G:45 , GLY G:46 , ALA G:47 , THR H:87 , SER H:88	BINDING SITE FOR RESIDUE SO4 H 201
5	AC5	SOFTWARE	HIS H:46 , PRO H:47 , ASP H:48 , THR H:49	BINDING SITE FOR RESIDUE SO4 H 202
6	AC6	SOFTWARE	LYS C:36 , TYR C:39 , GLU D:68 , HIS H:79	BINDING SITE FOR RESIDUE RU7 H 203

(no "SS Bond" information available for 4J8V)

(no "Cis Peptide Bond" information available for 4J8V)

(no "SAP(SNP)/Variant" information available for 4J8V)

(no "PROSITE Motif" information available for 4J8V)

(no "Exon" information available for 4J8V)

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:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4j8v A  38 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    47        57        67        77        87        97       107       117       127

Chain B from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4j8v B  21 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4j8v C  14 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119
                                    23        33        43        53        63        73        83        93       103       113

Chain D from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4j8v D  28 KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 122
                                    37        47        57        67        77        87        97       107       117

Chain E from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4j8v E  38 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 134
                                    47        57        67        77        87        97       107       117       127

Chain F from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4j8v F  16 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    25        35        45        55        65        75        85        95

Chain G from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4j8v G  14 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119
                                    23        33        43        53        63        73        83        93       103       113

Chain H from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4j8v H  28 KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 122
                                    37        47        57        67        77        87        97       107       117

Chain I from PDB  Type:DNA  Length:145
                                                                                                                                                                                 
                 4j8v I -72 ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGAATCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT  72
                                   -63       -53       -43       -33       -23       -13        -3         7        17        27        37        47        57        67

Chain J from PDB  Type:DNA  Length:145
                                                                                                                                                                                 
                 4j8v J -72 ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT  72
                                   -63       -53       -43       -33       -23       -13        -3         7        17        27        37        47        57        67

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4J8V)

(no "CATH Domain" information available for 4J8V)

(no "Pfam Domain" information available for 4J8V)

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

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