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(-) Description

Title :  APO ENZYME OF HUMAN POLYMERASE LAMBDA
 
Authors :  M. S. Liu, M. D. Tsai
Date :  30 Jun 15  (Deposition) - 24 Feb 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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

(-) 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 250-575
    Gene: POLL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE KAPPA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5CB1)

(-) Sites  (0, 0)

(no "Site" information available for 5CB1)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:543 -B:543

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1His A:321 -Leu A:322
2Gly A:508 -Ser A:509
3Gly B:481 -Pro B:482
4Gly B:508 -Ser B:509
5Gly B:546 -Pro B:547

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CB1)

(-) Exons   (0, 0)

(no "Exon" information available for 5CB1)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...eeeee........ee..eeeeee........hhhhhhhhhhhhhh.ee.....eeee..eeeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..ee.....eee........hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cb1 A 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 B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeeehhhhhh..ee..eeeeee........hhhhhhhhhhhhh..........eee..eeeeeeee.........eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee....eee....................hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cb1 B 331 SVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570
   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 5CB1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CB1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CB1)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Gly A:508 - Ser A:509   [ RasMol ]  
    Gly B:481 - Pro B:482   [ RasMol ]  
    Gly B:508 - Ser B:509   [ RasMol ]  
    Gly B:546 - Pro B:547   [ RasMol ]  
    His A:321 - Leu A:322   [ RasMol ]  
 
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  5cb1
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  DPOLL_HUMAN | Q9UGP5
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  2.7.7.7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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 5chg 5cj7 5cp2 5cr0 5cwr 5ddm 5ddy 5dkw 5iii 5iij 5iik 5iil 5iim 5iin 5iio

(-) Related Entries Specified in the PDB File

4w4p 4W4P CONTAINS THE SAME PROTEIN COMPLEXED WITH MNMGDCTP