3PZP - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HUMAN DNA POLYMERASE KAPPA EXTENDING OPPOSITE A CIS-SYN THYMINE DIMER

Authors :   R. Vasquez-Del Carpio, T. D. Silverstein, S. Lone, R. E. Johnson, S. Pr L. Prakash, A. K. Aggarwal

Date :   14 Dec 10 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.34

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

Keywords :   Dna Nucleotidyltransferase, Dna Binding Nucleotide Binding Magnesium Binding, Nucleus, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Vasquez-Del Carpio, T. D. Silverstein, S. Lone, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Role Of Human Dna Polymerase Kappa In Extension Opposite From A Cis-Syn Thymine Dimer.
J. Mol. Biol. V. 408 252 2011
PubMed-ID: 21354175 | Reference-DOI: 10.1016/J.JMB.2011.02.042

Molecule 1 - DNA POLYMERASE KAPPA
	Chains	:	A, B
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Plasmid	:	PBJ943
	Expression System Strain	:	BJ5464
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 19-528
	Gene	:	POLK, DINB1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DINB PROTEIN, DINP

*Molecule 2 - 5'-D(GPGPGPGPGPAPAPGPGPAPCPCPA)-3'**
	Chains	:	P, Q
	Engineered	:	YES
	Other Details	:	OLIGONUCLEOTIDE
	Synthetic	:	YES

*Molecule 3 - 5'-D(TPTPCPCP(TTD) PGPGPTPCPCPTPTPCPCPCPCPC)-3'**
	Chains	:	T, U
	Engineered	:	YES
	Other Details	:	OLIGONUCLEOTIDE
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	DTP	2	Ligand/Ion	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	TTD	2	Mod. Nucleotide	CIS-SYN CYCLOBUTANE THYMINE DIMER

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DTP	1	Ligand/Ion	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TTD	1	Mod. Nucleotide	CIS-SYN CYCLOBUTANE THYMINE DIMER

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	DTP	1	Ligand/Ion	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TTD	1	Mod. Nucleotide	CIS-SYN CYCLOBUTANE THYMINE DIMER

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MG A:2 , ALA A:26 , ASP A:107 , MET A:108 , ASP A:109 , 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 , DA P:13 , TTD T:6	BINDING SITE FOR RESIDUE DTP A 1
2	AC2	SOFTWARE	DTP A:1 , ASP A:107 , MET A:108 , ASP A:198	BINDING SITE FOR RESIDUE MG A 2
3	AC3	SOFTWARE	ARG A:352 , VAL A:354 , ILE A:357 , DC P:12	BINDING SITE FOR RESIDUE MG A 3
4	AC4	SOFTWARE	MG B:1 , ALA B:26 , ASP B:107 , MET B:108 , ALA B:110 , PHE B:111 , TYR B:112 , SER B:137 , THR B:138 , TYR B:141 , ARG B:144 , ALA B:151 , ASP B:198 , GLU B:199 , LYS B:328 , DA Q:13 , TTD U:6	BINDING SITE FOR RESIDUE DTP B 2
5	AC5	SOFTWARE	DTP B:2 , ASP B:107 , MET B:108 , ASP B:198	BINDING SITE FOR RESIDUE MG B 1
6	AC6	SOFTWARE	ARG B:352 , VAL B:354 , ILE B:357 , DC Q:12	BINDING SITE FOR RESIDUE MG B 4

(no "SS Bond" information available for 3PZP)

Asymmetric Unit

No.	Residues
1	Lys A:328	-	Pro A:329
2	Phe A:500	-	Pro A:501
3	Gly B:30	-	Leu B:31
4	Lys B:328	-	Pro B:329
5	Arg B:409	-	Asp B:410
6	Phe B:500	-	Pro B:501

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048886	S	423	R	POLK_HUMAN	Polymorphism	35257416	A/B	S	423	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048886	S	423	R	POLK_HUMAN	Polymorphism	35257416	A	S	423	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048886	S	423	R	POLK_HUMAN	Polymorphism	35257416	B	S	423	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UMUC	PS50173	UmuC domain profile.	POLK_HUMAN	103-358	2	A:103-358 B:103-358

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UMUC	PS50173	UmuC domain profile.	POLK_HUMAN	103-358	1	A:103-358 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UMUC	PS50173	UmuC domain profile.	POLK_HUMAN	103-358	1	- B:103-358

Asymmetric Unit (12, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000241436	1a	ENSE00002022143	chr5:74807581-74807739	159	POLK_HUMAN	-	0	0	-	-
1.4a	ENST00000241436	4a	ENSE00002160720	chr5:74842835-74842982	148	POLK_HUMAN	1-45	45	2	A:25-45 B:19-45	21 27
1.5b	ENST00000241436	5b	ENSE00001649227	chr5:74848297-74848416	120	POLK_HUMAN	46-85	40	2	A:46-85 B:46-85	40 40
1.7b	ENST00000241436	7b	ENSE00001643362	chr5:74865165-74865317	153	POLK_HUMAN	86-136	51	2	A:86-136 B:86-136	51 51
1.8b	ENST00000241436	8b	ENSE00000827223	chr5:74869563-74869694	132	POLK_HUMAN	137-180	44	2	A:137-180 B:137-180	44 44
1.9b	ENST00000241436	9b	ENSE00000827224	chr5:74872605-74872758	154	POLK_HUMAN	181-232	52	2	A:181-224 B:181-224	44 44
1.10a	ENST00000241436	10a	ENSE00000827225	chr5:74877034-74877273	240	POLK_HUMAN	232-312	81	2	A:281-312 B:282-312	32 31
1.11	ENST00000241436	11	ENSE00000827226	chr5:74879118-74879242	125	POLK_HUMAN	312-353	42	2	A:312-353 B:312-353	42 42
1.12	ENST00000241436	12	ENSE00000827227	chr5:74880585-74880751	167	POLK_HUMAN	354-409	56	2	A:354-409 B:354-409	56 56
1.13	ENST00000241436	13	ENSE00001004825	chr5:74882851-74882883	33	POLK_HUMAN	409-420	12	2	A:409-420 B:409-420	12 12
1.14a	ENST00000241436	14a	ENSE00000827228	chr5:74886169-74886265	97	POLK_HUMAN	420-452	33	2	A:420-452 B:420-452	33 33
1.15a	ENST00000241436	15a	ENSE00000827229	chr5:74889703-74889874	172	POLK_HUMAN	453-510	58	2	A:453-510 B:453-510	58 58
1.16a	ENST00000241436	16a	ENSE00001742078	chr5:74892047-74893003	957	POLK_HUMAN	510-829	320	2	A:510-520 B:510-518	11 9
1.17b	ENST00000241436	17b	ENSE00001614437	chr5:74893572-74893614	43	POLK_HUMAN	829-843	15	0	-	-
1.17l	ENST00000241436	17l	ENSE00001905813	chr5:74893759-74896969	3211	POLK_HUMAN	843-870	28	0	-	-

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:440
 aligned with POLK_HUMAN | Q9UBT6 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:496
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514      
           POLK_HUMAN    25 KAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEE 520
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhh...eeeee..eeeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh...........eeeeehhhhhhhhh.......eee..--------------------------------------------------------..eee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee....eeee.........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------UMUC  PDB: A:103-358 UniProt: 103-358                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4a            Exon 1.5b  PDB: A:46-85 UniProt: 46-85  Exon 1.7b  PDB: A:86-136 UniProt: 86-136           Exon 1.8b  PDB: A:137-180 UniProt: 137-180  ---------------------------------------------------Exon 1.10a  PDB: A:281-312 UniProt: 232-312 [INCOMPLETE]                         -----------------------------------------Exon 1.12  PDB: A:354-409 UniProt: 354-409              ----------Exon 1.14a  PDB: A:420-452       Exon 1.15a  PDB: A:453-510 UniProt: 453-510               ---------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:181-224 UniProt: 181-232          -------------------------------------------------------------------------------Exon 1.11  PDB: A:312-353 UniProt: 312-353-------------------------------------------------------Exon 1.13   -----------------------------------------------------------------------------------------Exon 1.16a  Transcript 1 (2)
                 3pzp A  25 KAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIK--------------------------------------------------------QNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEE 520
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224         -         -         -         -         -      |284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514      
                                                                                                                                                                                                                                 224                                                      281

Chain B from PDB  Type:PROTEIN  Length:443
 aligned with POLK_HUMAN | Q9UBT6 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:500
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518
           POLK_HUMAN    19 MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN 518
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhh...eeeee..ee...hhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.....eeee..eeee.hhhhhhhhh.......ee...---------------------------------------------------------..ee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh.............hhhhhhhhhhh.hhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee....ee..eeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------UMUC  PDB: B:103-358 UniProt: 103-358                                                                                                                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: B:19-45    Exon 1.5b  PDB: B:46-85 UniProt: 46-85  Exon 1.7b  PDB: B:86-136 UniProt: 86-136           Exon 1.8b  PDB: B:137-180 UniProt: 137-180  ---------------------------------------------------Exon 1.10a  PDB: B:282-312 UniProt: 232-312 [INCOMPLETE]                         -----------------------------------------Exon 1.12  PDB: B:354-409 UniProt: 354-409              ----------Exon 1.14a  PDB: B:420-452       Exon 1.15a  PDB: B:453-510 UniProt: 453-510               -------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: B:181-224 UniProt: 181-232          -------------------------------------------------------------------------------Exon 1.11  PDB: B:312-353 UniProt: 312-353-------------------------------------------------------Exon 1.13   -----------------------------------------------------------------------------------------1.16a     Transcript 1 (2)
                 3pzp B  19 MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIK---------------------------------------------------------NSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN 518
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218     |   -         -         -         -         -         -   |   288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518
                                                                                                                                                                                                                                       224                                                       282

Chain P from PDB  Type:DNA  Length:13
                                             
                 3pzp P   1 GGGGGAAGGACCA  13
                                    10

Chain Q from PDB  Type:DNA  Length:12
                                            
                 3pzp Q   2 GGGGAAGGACCA  13
                                    11

Chain T from PDB  Type:DNA  Length:15
                                               
                 3pzp T   4 CCtGGTCCTTCCCCC  18
                              |     13     
                              6-TTD

Chain U from PDB  Type:DNA  Length:14
                                              
                 3pzp U   4 CCtGGTCCTTCCCC  17
                              |     13    
                              6-TTD

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 3PZP)

(no "CATH Domain" information available for 3PZP)

(no "Pfam Domain" information available for 3PZP)

Asymmetric Unit(hide GO term definitions)

Chain A,B (POLK_HUMAN | Q9UBT6)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0042276	error-prone translesion synthesis	The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
	GO:0006297	nucleotide-excision repair, DNA gap filling	Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
	GO:0033683	nucleotide-excision repair, DNA incision	A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
	GO:0006296	nucleotide-excision repair, DNA incision, 5'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
	GO:0006283	transcription-coupled nucleotide-excision repair	The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
	GO:0019985	translesion synthesis	The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
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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
		Arg B:409 - Asp B:410	[ RasMol ]
		Gly B:30 - Leu B:31	[ RasMol ]
		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 ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3pzp
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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Access by UniProt ID/Accession number
	POLK_HUMAN \| Q9UBT6
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	2.7.7.7
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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Access by UniProt ID/Accession number
	POLK_HUMAN \| Q9UBT6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	POLK_HUMAN \| Q9UBT6	:	1t94 2lsi 2oh2 2w7o 2w7p 3in5 4ba9 4gk5 4u6p 4u7c 5t14

1t94	CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF HUMAN DNA POLYMERASE KAPPA
2oh2	TERNARY COMPLEX OF HUMAN DNA POLYMERASE KAPPA
3in5	STRUCTURE OF HUMAN DNA POLYMERASE KAPPA INSERTING DATP OPPOSITE AN 8-OXOG DNA LESION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (12, 24)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (19, 19)

Visualization

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Still Images

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Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File