4U6P - JenaLib

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Title :   STRUCTURAL MECHANISM OF ERROR-FREE BYPASS OF MAJOR BENZO[A]PYRENE ADDUCT BY HUMAN POLYMERASE KAPPA

Authors :   V. K. Jha, H. Ling

Date :   29 Jul 14 (Deposition) - 27 Jan 16 (Release) - 15 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.59

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	:	BL21PRARE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	POLK, DINB1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DINB PROTEIN,DINP

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

*Molecule 3 - DNA (5'-D(TPAPTPGPGPTPGPAPTPCPCPGPC)-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 (3, 9)

No.	Name	Count	Type	Full Name
1	DCT	2	Ligand/Ion	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
2	MG	6	Ligand/Ion	MAGNESIUM ION
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DCT	1	Ligand/Ion	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PGE	-1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	DCT	1	Ligand/Ion	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:352 , VAL A:354 , ILE A:357 , HOH A:713 , DA C:12 , HOH C:103	binding site for residue MG A 601
2	AC2	SOFTWARE	ASP A:107 , MET A:108 , ASP A:198 , MG A:603 , DCT A:604	binding site for residue MG A 602
3	AC3	SOFTWARE	ASP A:107 , ASP A:198 , GLU A:199 , MG A:602 , DCT A:604 , HOH A:745	binding site for residue MG A 603
4	AC4	SOFTWARE	ASP A:107 , ALA A:110 , SER A:137 , THR A:138 , TYR A:141 , ARG A:144 , ALA A:151 , ASP A:198 , LYS A:328 , MG A:602 , MG A:603 , HOH A:735 , HOH A:745 , DC C:13 , DG D:5	binding site for residue DCT A 604
5	AC5	SOFTWARE	LYS B:459 , LYS B:461 , HOH B:705 , DT P:10 , DG T:5 , DG T:6 , HOH T:105	binding site for residue PGE B 601
6	AC6	SOFTWARE	ARG B:352 , VAL B:354 , ILE B:357 , DA P:12	binding site for residue MG B 602
7	AC7	SOFTWARE	ASP B:107 , MET B:108 , ASP B:198 , MG B:604 , DCT B:605	binding site for residue MG B 603
8	AC8	SOFTWARE	ASP B:107 , GLU B:199 , MG B:603 , DCT B:605 , HOH B:722	binding site for residue MG B 604
9	AC9	SOFTWARE	ASP B:107 , MET B:108 , ALA B:110 , SER B:137 , THR B:138 , TYR B:141 , ARG B:144 , ASP B:198 , LYS B:328 , MG B:603 , MG B:604 , DC P:13 , DG T:5	binding site for residue DCT B 605

(no "SS Bond" information available for 4U6P)

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 4U6P)

(no "PROSITE Motif" information available for 4U6P)

(no "Exon" information available for 4U6P)

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.......eee...eee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee...hhhhhhhhhh..hhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u6p A  31 LDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN 518
                                    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 B 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.......eee...eee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee...hhhhhhhhhh..hhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u6p B  31 LDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN 518
                                    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
                                         
                 4u6p C   5 GCGGATCAC  13

Chain D from PDB  Type:DNA  Length:13
                                             
                 4u6p D   2 TATGGTGATCCGC  14
                                    11

Chain P from PDB  Type:DNA  Length:9
                                         
                 4u6p P   5 GCGGATCAC  13

Chain T from PDB  Type:DNA  Length:13
                                             
                 4u6p T   2 TATGGTGATCCGC  14
                                    11

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 4U6P)

(no "CATH Domain" information available for 4U6P)

(no "Pfam Domain" information available for 4U6P)

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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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Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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