4GP7 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   POLYNUCLEOTIDE KINASE

Authors :   L. K. Wang, U. Das, P. Smith, S. Shuman

Date :   20 Aug 12 (Deposition) - 14 Nov 12 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Polynucleotide Kinase Phosphatase, Rna Repair, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. K. Wang, U. Das, P. Smith, S. Shuman
Structure And Mechanism Of The Polynucleotide Kinase Component Of The Bacterial Pnkp-Hen1 Rna Repair System.
Rna V. 18 2277 2012
PubMed-ID: 23118415 | Reference-DOI: 10.1261/RNA.036061.112

Molecule 1 - METALLOPHOSPHOESTERASE
	Chains	:	A, B
	EC Number	:	2.7.1.78
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CTHE_2768
	Mutation	:	YES
	Organism Scientific	:	CLOSTRIDIUM THERMOCELLUM
	Organism Taxid	:	203119
	Strain	:	ATCC 27405 / DSM 1237

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 14)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CIT	1	Ligand/Ion	CITRIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
5	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CIT	1	Ligand/Ion	CITRIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:16 , SER A:17 , GLY A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , THR A:23 , ASP A:38 , ARG A:116 , ARG A:120 , ARG A:123 , MG A:1002 , HOH A:1129 , HOH A:1130 , HOH A:1131 , HOH A:1132 , HOH A:1151 , HOH A:1179 , HOH A:1181 , HOH A:1190	BINDING SITE FOR RESIDUE ATP A 1001
2	AC2	SOFTWARE	SER A:22 , ATP A:1001 , HOH A:1129 , HOH A:1130 , HOH A:1131	BINDING SITE FOR RESIDUE MG A 1002
3	AC3	SOFTWARE	ASN A:107 , ILE A:141 , ILE A:154 , ASN A:156 , HOH A:1154 , HOH A:1176 , ILE B:141 , LYS B:142	BINDING SITE FOR RESIDUE CIT A 1003
4	AC4	SOFTWARE	SER B:16 , SER B:17 , GLY B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , THR B:23 , ARG B:116 , ARG B:120 , MG B:1002 , HOH B:1118 , HOH B:1119 , HOH B:1120 , HOH B:1130 , HOH B:1133 , HOH B:1138 , HOH B:1139 , HOH B:1151	BINDING SITE FOR RESIDUE ATP B 1001
5	AC5	SOFTWARE	SER B:22 , ATP B:1001 , HOH B:1118 , HOH B:1119 , HOH B:1120	BINDING SITE FOR RESIDUE MG B 1002
6	AC6	SOFTWARE	PHE B:100 , ARG B:150 , TYR B:151	BINDING SITE FOR RESIDUE NA B 1003

(no "SS Bond" information available for 4GP7)

(no "Cis Peptide Bond" information available for 4GP7)

(no "SAP(SNP)/Variant" information available for 4GP7)

(no "PROSITE Motif" information available for 4GP7)

(no "Exon" information available for 4GP7)

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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee.....hhhhhhhhhhhhh.eeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhh..eeeee.hhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gp7 A   0 SmKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLmSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEmAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQmKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP 170
                             |       9        19        29        39    |   49        59        69        79        89   |    99       109       119       129       139       149       159       169 
                             |                                         44-MSE                                           93-MSE                                     137-MSE                             
                             1-MSE

Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....eeeeee.....hhhhhhhhhhhhh.eeehhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhh..eeeee.hhhhhhheeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gp7 B   0 SmKLTIPELSLVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLmSDDENDQTVTGAAFDVLHYIVSKRLQLGKLTVVDATNVQESARKPLIEmAKDYHCFPVAVVFNLPEKVCQERNKNRTDRQVEEYVIRKHTQQmKKSIKGLQREGFRYVYILNSPEEVEEVVFERQP 170
                             |       9        19        29        39    |   49        59        69        79        89   |    99       109       119       129       139       149       159       169 
                             1-MSE                                     44-MSE                                           93-MSE                                     137-MSE

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 4GP7)

(no "CATH Domain" information available for 4GP7)

(no "Pfam Domain" information available for 4GP7)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gp7)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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3ty5	LIG DOMAIN OF CTH PNKP
3ty8	LIG DOMAIN OF CTH PNKP
3ty9	LIG DOMAIN OF CTH PNKP
4drf	N-TERMINAL HEN1- C-TERMINAL LIG DOMAIN OF CTH HEN 1 PNKP
4e6n	N-TERMINAL HEN1- C-TERMINAL LIG DOMAIN OF CTH HEN 1 PNKP
4gp6

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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