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(-) Description

Title :  TERNARY CRYSTAL STRUCTURE OF POLYMERASE LAMBDA WITH A GA MISPAIR AT THE PRIMER TERMINUS WITH CA2+ IN THE ACTIVE
 
Authors :  M. S. Liu, M. D. Tsai
Date :  04 Sep 15  (Deposition) - 24 Feb 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B,C,D,E,F,P,T
Biol. Unit 1:  A,D,P,T  (1x)
Biol. Unit 2:  B,C,E,F  (1x)
Keywords :  Polymerase Lambda, Transferase, Transferase-Dna Complex (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

(-) Compounds

Molecule 1 - DNA POLYMERASE LAMBDA
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 249-575
    Gene: POLL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE KAPPA
 
Molecule 2 - DNA (5'-D(P*GP*CP*CP*G)-3')
    Chains: D, C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')
    Chains: P, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3')
    Chains: T, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFPT
Biological Unit 1 (1x): A  D  PT
Biological Unit 2 (1x):  BC EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG 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 , GLY A:508 , ASN A:513 , CA A:602 , HOH A:710 , DC P:6 , DG T:5binding site for residue DTP A 601
2AC2SOFTWAREASP A:427 , DTP A:601 , HOH A:744 , HOH A:747binding site for residue CA A 602
3AC3SOFTWARECYS A:300 , ILE A:302 , ILE A:305 , HOH A:786 , DC D:3 , HOH D:101binding site for residue CA A 603
4AC4SOFTWARECYS B:300 , ILE B:302 , ILE B:305 , DC C:3binding site for residue CA B 601
5AC5SOFTWARESER B:339 , ILE B:341 , ALA B:344 , DA E:5 , HOH E:103binding site for residue CA B 602
6AC6SOFTWAREARG B:386 , GLY B:416 , SER B:417 , ARG B:420 , GLY B:426 , ASP B:427 , ASP B:429 , TYR B:505 , PHE B:506 , GLY B:508 , ASN B:513 , CA B:604 , HOH B:702 , DC E:6 , DG F:5binding site for residue DTP B 603
7AC7SOFTWAREASP B:427 , ASP B:429 , DTP B:603 , HOH B:745binding site for residue CA B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DKW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:508 -Ser A:509
2Gly B:508 -Ser B:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DKW)

(-) Sequences/Alignments

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:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhh......eeee.hhhh....ee..eeeeee.........hhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee.......ee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dkw A 249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 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       546       556       566         
                                                                                                                                                                                                                                                                                                                          537|                             
                                                                                                                                                                                                                                                                                                                           546                             


Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhh..hhhhhh...hhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh.....eeeeehhhh....ee..eeeeee.........hhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee.......ee...hhhhhhhh......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dkw B 249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 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       546       556       566         
                                                                                                                                                                                                                                                                                                                          537|                             
                                                                                                                                                                                                                                                                                                                           546                             


Chain C from PDB  Type:DNA  Length:4
                                    
                 5dkw C   1 GCCG   4


Chain D from PDB  Type:DNA  Length:4
                                    
                 5dkw D   1 GCCG   4


Chain E from PDB  Type:DNA  Length:6
                                      
                 5dkw E   1 CAGTAC   6


Chain F from PDB  Type:DNA  Length:11
                                           
                 5dkw F   1 CGGCGGTACTG  11
                                    10 


Chain P from PDB  Type:DNA  Length:6
                                      
                 5dkw P   1 CAGTAC   6


Chain T from PDB  Type:DNA  Length:11
                                           
                 5dkw T   1 CGGCGGTACTG  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        DPOLL_HUMAN | Q9UGP5: 1nzp 1rzt 1xsl 1xsn 1xsp 2bcq 2bcr 2bcs 2bcu 2bcv 2gws 2jw5 2pfn 2pfo 2pfp 2pfq 3c5f 3c5g 3hw8 3hwt 3hx0 3mda 3mdc 3mgh 3mgi 3pml 3pmn 3pnc 3upq 3uq0 3uq2 4fo6 4k4g 4k4h 4k4i 4x5v 4xa5 4xq8 4xrh 4xus 5ca7 5cb1 5chg 5cj7 5cp2 5cr0 5cwr 5ddm 5ddy 5iii 5iij 5iik 5iil 5iim 5iin 5iio

(-) Related Entries Specified in the PDB File

5cb1 5CB1 CONTAINS THE SAME PROTEIN- APOENZYME