4U7C - JenaLib

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Title :   STRUCTURE OF DNA POLYMERASE KAPPA IN COMPLEX WITH BENZOPYRENE ADDUCTED DNA

Authors :   V. K. Jha, H. Ling

Date :   30 Jul 14 (Deposition) - 27 Jan 16 (Release) - 15 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Benzo[A]Pyrene-N2-Guanine, Dna Replication, Dna Damage Tolerance, Polymerase Kappa, Environment Pollution, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Jha, C. Bian, G. Xing, H. Ling
Structure And Mechanism Of Error-Free Replication Past The Major Benzo[A]Pyrene Adduct By Human Dna Polymerase Kappa.
Nucleic Acids Res. V. 44 4957 2016
PubMed-ID: 27034468 | Reference-DOI: 10.1093/NAR/GKW204

Molecule 1 - DNA POLYMERASE KAPPA
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 27-518
	Gene	:	POLK, DINB1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DINB PROTEIN,DINP

*Molecule 2 - DNA (5'-D(PGPCPGPGPAPTPCPAPG)-3')**
	Chains	:	C, P
	Engineered	:	YES
	Organism Scientific	:	UNIDENTIFIED
	Organism Taxid	:	32644
	Synthetic	:	YES

*Molecule 3 - DNA (5'-D(PAPTPGP(VKJ)PCPTPGPAPTPCPCPGPC)- 3')*
	Chains	:	D, T
	Engineered	:	YES
	Organism Scientific	:	UNIDENTIFIED
	Organism Taxid	:	32644
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	P	T
Biological Unit 1 (1x)	:	A		C	D
Biological Unit 2 (1x)	:		B			P	T

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	0KX	2	Ligand/Ion	2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	VKJ	2	Mod. Nucleotide	2'-DEOXY-N-[(7R,8S,9R,10S)-7,8,9-TRIHYDROXY-7,8,9,10-TETRAHYDROBENZO[PQR]TETRAPHEN-10-YL]GUANOSINE 5'-(DIHYDROGEN PHOSPHATE)

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	0KX	1	Ligand/Ion	2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	VKJ	1	Mod. Nucleotide	2'-DEOXY-N-[(7R,8S,9R,10S)-7,8,9-TRIHYDROXY-7,8,9,10-TETRAHYDROBENZO[PQR]TETRAPHEN-10-YL]GUANOSINE 5'-(DIHYDROGEN PHOSPHATE)

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	0KX	1	Ligand/Ion	2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	VKJ	1	Mod. Nucleotide	2'-DEOXY-N-[(7R,8S,9R,10S)-7,8,9-TRIHYDROXY-7,8,9,10-TETRAHYDROBENZO[PQR]TETRAPHEN-10-YL]GUANOSINE 5'-(DIHYDROGEN PHOSPHATE)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:107 , MET A:108 , ASP A:198 , 0KX A:602	binding site for residue MG A 601
02	AC2	SOFTWARE	ASP A:107 , MET A:108 , ALA A:110 , PHE A:111 , TYR A:112 , SER A:137 , THR A:138 , TYR A:141 , ARG A:144 , ASP A:198 , LYS A:328 , MG A:601 , DG C:13 , VKJ D:5	binding site for residue 0KX A 602
03	AC3	SOFTWARE	LYS A:459 , LYS A:461 , VAL A:467 , DA C:9	binding site for residue PEG A 603
04	AC4	SOFTWARE	GLY B:131 , SER B:132 , MET B:135 , PRO B:169 , VKJ T:5	binding site for residue EDO B 601
05	AC5	SOFTWARE	ASP B:107 , MET B:108 , ASP B:198 , 0KX B:603	binding site for residue MG B 602
06	AC6	SOFTWARE	ASP B:107 , MET B:108 , ALA B:110 , PHE B:111 , SER B:137 , THR B:138 , TYR B:141 , ARG B:144 , ASP B:198 , LYS B:328 , MG B:602 , DG P:13 , VKJ T:5	binding site for residue 0KX B 603
07	AC7	SOFTWARE	PHE B:171 , HOH B:726 , VKJ T:5	binding site for residue PEG B 604
08	AC8	SOFTWARE	TYR B:432 , LYS B:489 , HOH B:710	binding site for residue PEG B 605
09	AC9	SOFTWARE	THR A:44 , SER A:47 , PHE A:49 , TYR A:112 , SER A:134 , MET A:135 , SER A:137 , ALA A:151 , PRO A:153 , PRO A:169 , THR A:421 , ARG A:507 , 0KX A:602 , HOH A:708 , HOH A:722 , DG C:13 , DT D:3 , DC D:6 , HOH D:108	binding site for Di-nucleotide DG D 4 and VKJ D 5
10	AD1	SOFTWARE	TYR A:112 , MET A:135 , SER A:137 , ALA A:151 , PRO A:169 , GLU A:419 , THR A:421 , ARG A:507 , LEU A:508 , 0KX A:602 , HOH A:708 , HOH A:722 , DG C:13 , DG D:4 , DT D:7 , HOH D:101 , HOH D:108 , HOH D:109	binding site for Di-nucleotide VKJ D 5 and DC D 6
11	AD2	SOFTWARE	THR B:44 , SER B:47 , PHE B:49 , TYR B:112 , SER B:134 , MET B:135 , ALA B:151 , PRO B:153 , ILE B:156 , PHE B:171 , ARG B:507 , EDO B:601 , 0KX B:603 , PEG B:604 , HOH B:726 , DG P:13 , DT T:3 , DC T:6	binding site for Di-nucleotide DG T 4 and VKJ T 5
12	AD3	SOFTWARE	TYR B:112 , MET B:135 , ALA B:151 , PHE B:171 , GLU B:419 , THR B:421 , ARG B:507 , LEU B:508 , EDO B:601 , 0KX B:603 , PEG B:604 , HOH B:712 , HOH B:726 , DG P:13 , DG T:4 , DT T:7	binding site for Di-nucleotide VKJ T 5 and DC T 6

(no "SS Bond" information available for 4U7C)

Asymmetric Unit

No.	Residues
1	Lys A:328	-	Pro A:329
2	Phe A:500	-	Pro A:501
3	Lys B:328	-	Pro B:329
4	Phe B:500	-	Pro B:501

(no "SAP(SNP)/Variant" information available for 4U7C)

(no "PROSITE Motif" information available for 4U7C)

(no "Exon" information available for 4U7C)

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:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh...eeee....eeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhh......ee....eeeeehhhhhhhhh..hhhh.eee....eee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh.......eee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u7c A  32 DKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN 518
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  ||   287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517 
                                                                                                                                                                                                                          224|                                                                                                                                                                                                                                             
                                                                                                                                                                                                                           281

Chain B from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh...eeee....eeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhh......ee....eeeeehhhhhhhhh..hhhh.eee...eee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh.......eee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u7c B  31 LDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFP 517
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   ||  287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517
                                                                                                                                                                                                                           224|                                                                                                                                                                                                                                           
                                                                                                                                                                                                                            282

Chain C from PDB  Type:DNA  Length:9
                                         
                 4u7c C   5 GCGGATCAG  13

Chain D from PDB  Type:DNA  Length:13
                                             
                 4u7c D   2 ATGxCTGATCCGC  14
                               |    11   
                               5-VKJ

Chain P from PDB  Type:DNA  Length:9
                                         
                 4u7c P   5 GCGGATCAG  13

Chain T from PDB  Type:DNA  Length:13
                                             
                 4u7c T   2 ATGxCTGATCCGC  14
                               |    11   
                               5-VKJ

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 4U7C)

(no "CATH Domain" information available for 4U7C)

(no "Pfam Domain" information available for 4U7C)

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
		0KX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Lys A:328 - Pro A:329	[ RasMol ]
		Lys B:328 - Pro B:329	[ RasMol ]
		Phe A:500 - Pro A:501	[ RasMol ]
		Phe B:500 - Pro B:501	[ RasMol ]

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	4u7c
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	2.7.7.7
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	POLK_HUMAN \| Q9UBT6	:	1t94 2lsi 2oh2 2w7o 2w7p 3in5 3pzp 4ba9 4gk5 4u6p 5t14

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (19, 19)

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