2GWS | PD0806 - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE LAMBDA WITH A G/G MISMATCH IN THE PRIMER TERMINUS

Authors :   M. Garcia-Diaz, A. J. Picher, K. Bebenek, L. C. Pedersen, T. A. Kunkel, L

Date :   05 May 06 (Deposition) - 05 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,D,E,F,G,H,I,J,K,L,M,N,P,Q,R,T
Biol. Unit 1: A,D,P,T  (1x)
Biol. Unit 2: E,F,G,H  (1x)
Biol. Unit 3: I,J,K,L  (1x)
Biol. Unit 4: M,N,Q,R  (1x)

Keywords :   Dna Polymerase Lambda, Family X, Mismatch Extension, Mutagenesis, Nhej, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Picher, M. Garcia-Diaz, K. Bebenek, L. C. Pedersen, T. A. Kunkel, L. Blanco
Promiscuous Mismatch Extension By Human Dna Polymerase Lambda.
Nucleic Acids Res. V. 34 3259 2006
PubMed-ID: 16807316 | Reference-DOI: 10.1093/NAR/GKL377

*Molecule 1 - 5'-D(CPGPGPCPAPGPCPGPCPAPC)-3'**
	Chains	:	T, F, J, N
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(GPTPGPCPGPG)-3'*
	Chains	:	P, G, K, R
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'-D(PGPCPCPG)-3'*
	Chains	:	D, H, L, Q
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - DNA POLYMERASE LAMBDA
	Chains	:	A, E, I, M
	EC Number	:	2.7.7.7, 4.2.99.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	POLL
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	POL LAMBDA, DNA POLYMERASE KAPPA, DNA POLYMERASE BETA-2, POL BETA2

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric Unit	:	A	D	E	F	G	H	I	J	K	L	M	N	P	Q	R	T
Biological Unit 1 (1x)	:	A	D											P			T
Biological Unit 2 (1x)	:			E	F	G	H
Biological Unit 3 (1x)	:							I	J	K	L
Biological Unit 4 (1x)	:											M	N		Q	R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	CAC	3	Ligand/Ion	CACODYLATE ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	NA	8	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CAC	1	Ligand/Ion	CACODYLATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CAC	-1	Ligand/Ion	CACODYLATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:339 , ILE A:341 , ALA A:344 , HOH A:959 , DG P:5 , HOH P:423	BINDING SITE FOR RESIDUE NA A 940
02	AC2	SOFTWARE	SER E:339 , ILE E:341 , ALA E:344 , HOH E:2821 , DG G:5 , HOH G:262	BINDING SITE FOR RESIDUE NA E 941
03	AC3	SOFTWARE	SER I:339 , ILE I:341 , ALA I:344 , DG K:5 , HOH K:648	BINDING SITE FOR RESIDUE NA I 942
04	AC4	SOFTWARE	SER M:339 , ILE M:341 , ALA M:344 , HOH M:1033 , DG R:5 , HOH R:33	BINDING SITE FOR RESIDUE NA M 943
05	AC5	SOFTWARE	HOH D:634 , HOH T:631 , HOH T:632 , HOH T:633 , HOH T:635 , HOH T:636	BINDING SITE FOR RESIDUE NA T 944
06	AC6	SOFTWARE	DG P:5 , DG P:6 , HOH P:282 , DG T:6 , HOH T:507 , HOH T:568	BINDING SITE FOR RESIDUE NA P 945
07	AC7	SOFTWARE	DG F:2 , DG F:3 , HOH F:754 , HOH F:756 , HOH F:757 , HOH F:758 , HOH F:759 , HOH H:755	BINDING SITE FOR RESIDUE MG F 946
08	AC8	SOFTWARE	ASN M:340 , HOH M:1033	BINDING SITE FOR RESIDUE NA M 947
09	AC9	SOFTWARE	HOH N:2834 , HOH N:2835 , HOH Q:805	BINDING SITE FOR RESIDUE NA Q 948
10	BC1	SOFTWARE	DC D:3 , DG D:4 , DC N:1 , DC Q:3 , DG Q:4	BINDING SITE FOR RESIDUE CAC D 949
11	BC2	SOFTWARE	DG H:4	BINDING SITE FOR RESIDUE CAC H 950
12	BC3	SOFTWARE	DG J:2 , DG J:3 , DG L:1	BINDING SITE FOR RESIDUE CAC J 951
13	BC4	SOFTWARE	THR A:555 , GLU A:556	BINDING SITE FOR RESIDUE CL A 952
14	BC5	SOFTWARE	TYR M:505 , HOH M:1014 , DA N:5 , DG R:6	BINDING SITE FOR RESIDUE EDO N 2801

Asymmetric Unit

No.	Residues
1	A:543	-	M:543
2	E:543	-	I:543

Asymmetric Unit

No.	Residues
1	Gly A:508	-	Ser A:509
2	Gly E:508	-	Ser E:509
3	Gly I:508	-	Ser I:509
4	Gly M:508	-	Ser M:509

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020269	R	438	W	DPOLL_HUMAN	Polymorphism	3730477	A/E/I/M	R	438	W

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_020269	R	438	W	DPOLL_HUMAN	Polymorphism	3730477	A	R	438	W

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_020269	R	438	W	DPOLL_HUMAN	Polymorphism	3730477	E	R	438	W

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020269	R	438	W	DPOLL_HUMAN	Polymorphism	3730477	I	R	438	W

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020269	R	438	W	DPOLL_HUMAN	Polymorphism	3730477	M	R	438	W

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_X	PS00522	DNA polymerase family X signature.	DPOLL_HUMAN	416-435	4	A:416-435 E:416-435 I:416-435 M:416-435

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_X	PS00522	DNA polymerase family X signature.	DPOLL_HUMAN	416-435	1	A:416-435 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_X	PS00522	DNA polymerase family X signature.	DPOLL_HUMAN	416-435	1	- E:416-435 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_X	PS00522	DNA polymerase family X signature.	DPOLL_HUMAN	416-435	1	- - I:416-435 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_X	PS00522	DNA polymerase family X signature.	DPOLL_HUMAN	416-435	1	- - - M:416-435

Asymmetric Unit (5, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1k	ENST00000370169	1k	ENSE00001451987	chr10:103347178-103347003	176	DPOLL_HUMAN	1-39	39	0	-	-
1.3	ENST00000370169	3	ENSE00001731892	chr10:103345913-103345619	295	DPOLL_HUMAN	39-137	99	0	-	-
1.4b	ENST00000370169	4b	ENSE00001100422	chr10:103345235-103345073	163	DPOLL_HUMAN	137-191	55	0	-	-
1.5e	ENST00000370169	5e	ENSE00001617344	chr10:103344676-103344359	318	DPOLL_HUMAN	192-297	106	4	A:249-297 E:250-297 I:250-297 M:250-297	49 48 48 48
1.6b	ENST00000370169	6b	ENSE00002151653	chr10:103343438-103343265	174	DPOLL_HUMAN	298-355	58	4	A:298-355 E:298-355 I:298-355 M:298-355	58 58 58 58
1.7b	ENST00000370169	7b	ENSE00001593760	chr10:103342648-103342520	129	DPOLL_HUMAN	356-398	43	4	A:356-398 E:356-398 I:356-398 M:356-398	43 43 43 43
1.8c	ENST00000370169	8c	ENSE00001691940	chr10:103340173-103340005	169	DPOLL_HUMAN	399-455	57	4	A:399-455 E:399-455 I:399-455 M:399-455	57 57 57 57
1.9g	ENST00000370169	9g	ENSE00001451993	chr10:103339574-103338639	936	DPOLL_HUMAN	455-575	121	4	A:455-575 E:455-575 I:455-575 M:455-575	121 121 121 121

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:327
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:327
                                   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       528       538       548       558       568       
          DPOLL_HUMAN   249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d2gwsa1 A:249-328 DNA polymerase lambda                                         d2gwsa2 A:329-385 DNA polymerase lambda                  d2gwsa3 A:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains 2gwsA01 A:249-331  [code=1.10.150.110, no name defined]                            2gwsA02 A:332-385                                     2gwsA03 A:386-508 Beta Polymerase, domain 2                                                                                2gwsA04 A:509-575 Beta Polymerase, domain 3                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee.........hhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..ee...........ee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: A:249-297 UniProt: 192-297       Exon 1.6b  PDB: A:298-355 UniProt: 298-355                Exon 1.7b  PDB: A:356-398 UniProt: 356-398 Exon 1.8c  PDB: A:399-455 UniProt: 399-455               ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9g  PDB: A:455-575 UniProt: 455-575                                                                                Transcript 1 (2)
                 2gws A 249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   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       528       538       548       558       568

Chain D from PDB  Type:DNA  Length:4
                                    
                 2gws D   1 GCCG   4

Chain E from PDB  Type:PROTEIN  Length:326
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:326
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569      
          DPOLL_HUMAN   250 TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d2gwse1 E:250-328 DNA polymerase lambda                                        d2gwse2 E:329-385 DNA polymerase lambda                  d2gwse3 E:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains 2gwsE01 E:250-331  [code=1.10.150.110, no name defined]                           2gwsE02 E:332-385                                     2gwsE03 E:386-508 Beta Polymerase, domain 2                                                                                2gwsE04 E:509-575 Beta Polymerase, domain 3                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh.hhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee.........hhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..ee................hhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: E:250-297 UniProt: 192-297      Exon 1.6b  PDB: E:298-355 UniProt: 298-355                Exon 1.7b  PDB: E:356-398 UniProt: 356-398 Exon 1.8c  PDB: E:399-455 UniProt: 399-455               ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9g  PDB: E:455-575 UniProt: 455-575                                                                                Transcript 1 (2)
                 2gws E 250 TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569

Chain F from PDB  Type:DNA  Length:11
                                           
                 2gws F   1 CGGCAGCGCAC  11
                                    10

Chain G from PDB  Type:DNA  Length:6
                                      
                 2gws G   1 GTGCGG   6

Chain H from PDB  Type:DNA  Length:4
                                    
                 2gws H   1 GCCG   4

Chain I from PDB  Type:PROTEIN  Length:326
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:326
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569      
          DPOLL_HUMAN   250 TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d2gwsi1 I:250-328 DNA polymerase lambda                                        d2gwsi2 I:329-385 DNA polymerase lambda                  d2gwsi3 I:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains 2gwsI01 I:250-331  [code=1.10.150.110, no name defined]                           2gwsI02 I:332-385                                     2gwsI03 I:386-508 Beta Polymerase, domain 2                                                                                2gwsI04 I:509-575 Beta Polymerase, domain 3                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhh...hhhhhh...hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee........hhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee...............ee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: I:250-297 UniProt: 192-297      Exon 1.6b  PDB: I:298-355 UniProt: 298-355                Exon 1.7b  PDB: I:356-398 UniProt: 356-398 Exon 1.8c  PDB: I:399-455 UniProt: 399-455               ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9g  PDB: I:455-575 UniProt: 455-575                                                                                Transcript 1 (2)
                 2gws I 250 TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569

Chain J from PDB  Type:DNA  Length:11
                                           
                 2gws J   1 CGGCAGCGCAC  11
                                    10

Chain K from PDB  Type:DNA  Length:6
                                      
                 2gws K   1 GTGCGG   6

Chain L from PDB  Type:DNA  Length:4
                                    
                 2gws L   1 GCCG   4

Chain M from PDB  Type:PROTEIN  Length:326
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:326
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569      
          DPOLL_HUMAN   250 TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains d2gwsm1 M:250-328 DNA polymerase lambda                                        d2gwsm2 M:329-385 DNA polymerase lambda                  d2gwsm3 M:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains 2gwsM01 M:250-331  [code=1.10.150.110, no name defined]                           2gwsM02 M:332-385                                     2gwsM03 M:386-508 Beta Polymerase, domain 2                                                                                2gwsM04 M:509-575 Beta Polymerase, domain 3                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee.........hhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..ee...........ee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: M:250-297 UniProt: 192-297      Exon 1.6b  PDB: M:298-355 UniProt: 298-355                Exon 1.7b  PDB: M:356-398 UniProt: 356-398 Exon 1.8c  PDB: M:399-455 UniProt: 399-455               ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9g  PDB: M:455-575 UniProt: 455-575                                                                                Transcript 1 (2)
                 2gws M 250 TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569

Chain N from PDB  Type:DNA  Length:11
                                           
                 2gws N   1 CGGCAGCGCAC  11
                                    10

Chain P from PDB  Type:DNA  Length:6
                                      
                 2gws P   1 GTGCGG   6

Chain Q from PDB  Type:DNA  Length:4
                                    
                 2gws Q   1 GCCG   4

Chain R from PDB  Type:DNA  Length:6
                                      
                 2gws R   1 GTGCGG   6

Chain T from PDB  Type:DNA  Length:11
                                           
                 2gws T   1 CGGCAGCGCAC  11
                                    10

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: SAM domain-like (639)

Superfamily: DNA polymerase beta, N-terminal domain-like (205)

Family: DNA polymerase beta, N-terminal domain-like (183)

Protein domain: DNA polymerase lambda (24)

Human (Homo sapiens) [TaxId: 9606] (24)

1a	d2gwsa1	A:249-328
1b	d2gwse1	E:250-328
1c	d2gwsi1	I:250-328
1d	d2gwsm1	M:250-328

Superfamily: PsbU/PolX domain-like (218)

Family: DNA polymerase beta-like, second domain (190)

Protein domain: DNA polymerase lambda (23)

Human (Homo sapiens) [TaxId: 9606] (23)

2a	d2gwsa2	A:329-385
2b	d2gwse2	E:329-385
2c	d2gwsi2	I:329-385
2d	d2gwsm2	M:329-385

Class: Alpha and beta proteins (a+b) (23004)

Fold: Nucleotidyltransferase (287)

Superfamily: Nucleotidyltransferase (287)

Family: DNA polymerase beta-like (218)

Protein domain: DNA polymerase lambda (23)

Human (Homo sapiens) [TaxId: 9606] (23)

3a	d2gwsa3	A:386-575
3b	d2gwse3	E:386-575
3c	d2gwsi3	I:386-575
3d	d2gwsm3	M:386-575

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Beta Polymerase; domain 2 (187)

Homologous Superfamily: Beta Polymerase, domain 2 (183)

[unclassified] (117)

1a	2gwsA03	A:386-508
1b	2gwsE03	E:386-508
1c	2gwsI03	I:386-508
1d	2gwsM03	M:386-508

Topology: Beta Polymerase; domain 3 (161)

Homologous Superfamily: Beta Polymerase, domain 3 (161)

[unclassified] (116)

2a	2gwsA04	A:509-575
2b	2gwsE04	E:509-575
2c	2gwsI04	I:509-575
2d	2gwsM04	M:509-575

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: [code=1.10.150.110, no name defined] (150)

[unclassified] (116)

3a	2gwsA01	A:249-331
3b	2gwsE01	E:250-331
3c	2gwsI01	I:250-331
3d	2gwsM01	M:250-331

Homologous Superfamily: 5' to 3' exonuclease, C-terminal subdomain (384)

[unclassified] (230)

4a	2gwsA02	A:332-385
4b	2gwsE02	E:332-385
4c	2gwsI02	I:332-385
4d	2gwsM02	M:332-385

(no "Pfam Domain" information available for 2GWS)

Asymmetric Unit(hide GO term definitions)

Chain A,E,I,M (DPOLL_HUMAN | Q9UGP5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0034061	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 nucleic acid template and a 3'hydroxyl group.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
	GO:0016446	somatic hypermutation of immunoglobulin genes	Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
cellular component
	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.

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	2gws
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	2.7.7.7
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	4.2.99.-
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(no "Related Entries Specified in the PDB File" available for 2GWS)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (14, 14)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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Exons (5, 20)

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SCOP Domains (3, 12)

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