5DDY - JenaLib

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Title :   BINARY COMPLEX OF HUMAN POLYMERASE LAMBDA WITH DCTP

Authors :   M. S. Liu, M. D. Tsai

Date :   15 Aug 14 (Deposition) - 24 Feb 16 (Release) - 09 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.36

Chains :   Asym. Unit : A,C,E,G
Biol. Unit 1: A  (1x)
Biol. Unit 2: C  (1x)
Biol. Unit 3: E  (1x)
Biol. Unit 4: G  (1x)

Keywords :   Polymerase Lambda, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Liu, H. Y. Tsai, X. X. Liu, M. C. Ho, W. J. Wu, M. D. Tsai
Structural Mechanism For The Fidelity Modulation Of Dna Polymerase Lambda
J. Am. Chem. Soc. V. 138 2389 2016
PubMed-ID: 26836966 | Reference-DOI: 10.1021/JACS.5B13368

Molecule 1 - DNA POLYMERASE LAMBDA
	Chains	:	A, C, E, G
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 242-575
	Gene	:	POLL
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE KAPPA

		1	2	3	4
Asymmetric Unit	:	A	C	E	G
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		C
Biological Unit 3 (1x)	:			E
Biological Unit 4 (1x)	:				G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	DCP	4	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	MN	8	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DCP	1	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DCP	1	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	DCP	1	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	DCP	1	Ligand/Ion	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:416 , SER A:417 , ASP A:427 , ASP A:429 , DCP A:603	binding site for residue MG A 601
02	AC2	SOFTWARE	ASP A:427 , ASP A:429 , ASP A:490 , DCP A:603	binding site for residue MN A 602
03	AC3	SOFTWARE	ARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , TYR A:505 , PHE A:506 , THR A:507 , GLY A:508 , ASN A:513 , MG A:601 , MN A:602	binding site for residue DCP A 603
04	AC4	SOFTWARE	SER A:339 , ILE A:341 , ALA A:344	binding site for residue MN A 604
05	AC5	SOFTWARE	GLY C:416 , SER C:417 , ASP C:427 , ASP C:429 , DCP C:603	binding site for residue MG C 601
06	AC6	SOFTWARE	ASP C:427 , ASP C:429 , ASP C:490 , DCP C:603	binding site for residue MN C 602
07	AC7	SOFTWARE	ARG C:386 , GLY C:416 , SER C:417 , ARG C:420 , GLY C:426 , ASP C:427 , ASP C:429 , TYR C:505 , PHE C:506 , GLY C:508 , ASN C:513 , MG C:601 , MN C:602	binding site for residue DCP C 603
08	AC8	SOFTWARE	SER C:339 , HOH C:701	binding site for residue MN C 604
09	AC9	SOFTWARE	GLY E:416 , SER E:417 , ASP E:427 , ASP E:429 , DCP E:603	binding site for residue MG E 601
10	AD1	SOFTWARE	ASP E:427 , ASP E:429 , ASP E:490 , DCP E:603	binding site for residue MN E 602
11	AD2	SOFTWARE	ARG E:386 , SER E:417 , ARG E:420 , GLY E:426 , ASP E:427 , ASP E:429 , TYR E:505 , PHE E:506 , GLY E:508 , MG E:601 , MN E:602	binding site for residue DCP E 603
12	AD3	SOFTWARE	SER E:339 , ILE E:341	binding site for residue MN E 604
13	AD4	SOFTWARE	GLY G:416 , SER G:417 , ASP G:427 , ASP G:429 , DCP G:603	binding site for residue MG G 601
14	AD5	SOFTWARE	ASP G:427 , ASP G:429 , ASP G:490 , DCP G:603	binding site for residue MN G 602
15	AD6	SOFTWARE	ARG G:386 , SER G:417 , ARG G:420 , GLY G:426 , ASP G:427 , ASP G:429 , TYR G:505 , PHE G:506 , THR G:507 , GLY G:508 , ASN G:513 , MG G:601 , MN G:602	binding site for residue DCP G 603
16	AD7	SOFTWARE	SER G:339 , ILE G:341 , ALA G:344	binding site for residue MN G 604

Asymmetric Unit

No.	Residues
1	A:543	-	G:543
2	C:543	-	E:543

Asymmetric Unit

No.	Residues
1	His A:321	-	Leu A:322
2	Gly A:508	-	Ser A:509
3	Leu C:325	-	Asp C:326
4	Gly C:508	-	Ser C:509
5	Gly E:508	-	Ser E:509
6	Gly E:546	-	Pro E:547
7	Gly G:481	-	Pro G:482
8	Gly G:483	-	Arg G:484
9	Gly G:508	-	Ser G:509
10	Gly G:546	-	Pro G:547

(no "SAP(SNP)/Variant" information available for 5DDY)

(no "PROSITE Motif" information available for 5DDY)

(no "Exon" information available for 5DDY)

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
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.....hhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhh.....eeee.........ee..eeeeee........hhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh...eee....eee..ee.....eee........hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ddy 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 C from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhhhhh..........hhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhh..hhhhhhh..hhhhhh..eehhhhhhhhhhhhhhhhhhh...eeee.hhhhhh..ee.eeeeeee........hhhhhhhhhhhhh...........ee..eeee..eee.......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee....................hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ddy C 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 E from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....hhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeee.........ee..eeeeee........hhhhhhhhhhhhh.....eee...ee..eeeeeeee.........eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh...eee....eee...............ee...hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ddy E 332 VPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571

Chain G from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....hhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeee.............eeeeee.........hhhhhhhhhhhh..eeeeee...ee..eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee....eee...............ee...hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ddy G 332 VPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5DDY)

(no "CATH Domain" information available for 5DDY)

(no "Pfam Domain" information available for 5DDY)

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	Cis Peptide Bonds
		Gly A:508 - Ser A:509	[ RasMol ]
		Gly C:508 - Ser C:509	[ RasMol ]
		Gly E:508 - Ser E:509	[ RasMol ]
		Gly E:546 - Pro E:547	[ RasMol ]
		Gly G:481 - Pro G:482	[ RasMol ]
		Gly G:483 - Arg G:484	[ RasMol ]
		Gly G:508 - Ser G:509	[ RasMol ]
		Gly G:546 - Pro G:547	[ RasMol ]
		His A:321 - Leu A:322	[ RasMol ]
		Leu C:325 - Asp C:326	[ RasMol ]

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	5ddy
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5ddm	5DDM CONTAINS HUMAN DNA POLYMERASE LAMBDA- APOENZYME AND COMPLEX WITH 6 PAIRED DNA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (16, 16)

SS Bonds (2, 2)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (17, 17)

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