Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ACCESSORY SUBUNIT OF MURINE MITOCHONDRIAL POLYMERASE GAMMA
 
Authors :  J. A. Carrodeguas, K. Theis, D. F. Bogenhagen, C. Kisker
Date :  01 Nov 00  (Deposition) - 14 Mar 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Intermolecular Four Helix Bundle, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Carrodeguas, K. Theis, D. F. Bogenhagen, C. Kisker
Crystal Structure And Deletion Analysis Show That The Accessory Subunit Of Mammalian Dna Polymerase Gamma, Pol Gamma B, Functions As A Homodimer.
Mol. Cell V. 7 43 2001
PubMed-ID: 11172710  |  Reference-DOI: 10.1016/S1097-2765(01)00153-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DNA POLYMERASE GAMMA SUBUNIT B
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA4Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:93 , ARG A:96 , VAL A:99 , HOH A:911 , HOH A:920 , HOH A:978BINDING SITE FOR RESIDUE NA A 901
2AC2SOFTWAREVAL C:93 , ARG C:96 , VAL C:99 , HOH C:982 , HOH D:968BINDING SITE FOR RESIDUE NA C 902
3AC3SOFTWAREHOH A:1009 , VAL B:93 , ARG B:96 , VAL B:99 , HOH B:942 , HOH B:992BINDING SITE FOR RESIDUE NA B 903
4AC4SOFTWAREVAL D:93 , ARG D:96 , VAL D:99BINDING SITE FOR RESIDUE NA D 904
5AC5SOFTWAREASP C:103 , HIS C:106 , ARG D:81 , GLU D:207 , LYS D:208 , THR D:209 , ASP D:317 , HOH D:919 , HOH D:1018BINDING SITE FOR RESIDUE GOL D 5
6AC6SOFTWAREASP A:103 , HIS A:106 , ARG B:81 , GLU B:207 , LYS B:208 , THR B:209 , ASP B:317 , HOH B:910 , HOH B:982BINDING SITE FOR RESIDUE GOL B 6

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G5I)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:178 -Pro A:179
2Leu B:178 -Pro B:179
3Leu C:178 -Pro C:179
4Leu D:178 -Pro D:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G5I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G5I)

(-) Exons   (0, 0)

(no "Exon" information available for 1G5I)

(-) 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:405
 aligned with DPOG2_MOUSE | Q9QZM2 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                            459          
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450        |-         
          DPOG2_MOUSE    41 EALVDLCRRRHFFSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPGSSQPRDSAFRLVSPESIREILQDREPSKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVSNSNQTPSSVTRVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQLAENSFARKKSLQRKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNV----------   -
               SCOP domains d1g5ia2 A:41-330 The aaRS-like accessory subunit of mitochondrial polymerase gamma, N-termina   l domain                                                                                                                                                                                                      d1g5ia1 A:343-469 The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain                          SCOP domains
               CATH domains 1g5iA01 A:41-353 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                     1g5iA02 A:354-469  [code=3.40.50.800, no name defined]                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eee.....ee...........eeehhhhhhhhh..---hhhhhhhhhhhhhhhheee...hhhhhhhhhhhhhhhh.....eeeeeeeeeeeee.---------.eeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeee.....eeeeeeeee..eeeeeeeeeeeehhhhhhhh..hhhhh.eee..eee..eeeeeeeehhhhhhhhhhhhee.------------..ee..........eeeee...hhhhhhhhhhhhhhhhhhh...eehhhhh....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g5i A  41 EALVDLCRRRHFLSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPGSSQPRDSAFRLVSPESIREILQD---SKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVS---------TRVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQL------------RKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNVAAALDHHHHH 469
                                    50        60        70        80        90       100       110       120       130  |   |140       150       160       170       180       190  |      -  |    210       220       230       240       250       260       270       280       290       300       310       320       330         -  |    350       360       370       380       390       400       410       420       430       440       450       460         
                                                                                                                      133 137                                                     193       203                                                                                                                            330          343                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:397
 aligned with DPOG2_MOUSE | Q9QZM2 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:421
                                                                                                                                                                                                                                                                                                                                                                                                                                                             459 
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459 
          DPOG2_MOUSE    40 REALVDLCRRRHFFSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPGSSQPRDSAFRLVSPESIREILQDREPSKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVSNSNQTPSSVTRVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQLAENSFARKKSLQRKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNV-   -
               SCOP domains d1g5ib2 B:40-332 The aaRS-like accessory subunit of mitochondrial polym    erase gamma, N-terminal domain                                                                                                                                                                                                      d1g5ib1 B:343-460 The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain                 SCOP domains
               CATH domains 1g5iB01 B:40-353 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                      1g5iB02 B:354-460  [code=3.40.50.800, no name defined]                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eee.....ee..----.....eeehhhhhhhhhhh...hhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhh.....eeeeeeeeeeee..----------.eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeee.....eeeeeeeee..eeeeeeeeeeeehhhhhhhh..hhhhh.eee..eee..eeeeeeeehhhhhhhhhhhhee...----------..ee..........eeeee...hhhhhhhhhhhhhhhhhhh...eehhhhh....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g5i B  40 REALVDLCRRRHFLSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPG----RDSAFRLVSPESIREILQDREPSKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVS----------RVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQLAE----------RKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNVA 460
                                    49        59        69        79        89        99       109|    | 119       129       139       149       159       169       179       189   |     -    |  209       219       229       239       249       259       269       279       289       299       309       319       329  |      -   |   349       359       369       379       389       399       409       419       429       439       449       459 
                                                                                                110  115                                                                           193        204                                                                                                                             332        343                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:405
 aligned with DPOG2_MOUSE | Q9QZM2 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                            459          
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450        |-         
          DPOG2_MOUSE    41 EALVDLCRRRHFFSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPGSSQPRDSAFRLVSPESIREILQDREPSKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVSNSNQTPSSVTRVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQLAENSFARKKSLQRKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNV----------   -
               SCOP domains d1g5ic2 C:41-330 The aaRS-like accessory subunit of mitochondrial polymerase gamma, N-termina   l domain                                                                                                                                                                                                      d1g5ic1 C:343-469 The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain                          SCOP domains
               CATH domains 1g5iC01 C:41-353 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                     1g5iC02 C:354-469  [code=3.40.50.800, no name defined]                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eee.....ee...........eeehhhhhhh....---hhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhh.....eeeeeeeeeeeee.---------.eeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeee.....eeeeeeeee..eeeeeeeeeeeehhhhhhhh..hhhhh.eee..eee..eeeeeeeehhhhhhhhhhhhee.------------..ee..........eeeee...hhhhhhhhhhhhhhhhhhh...eee.hhh....hhhhhhhhhhhh...eeeeehhhhhhh.eeeeee.....eeeee..hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g5i C  41 EALVDLCRRRHFLSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPGSSQPRDSAFRLVSPESIREILQD---SKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVS---------TRVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQL------------RKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNVAAALDHHHHH 469
                                    50        60        70        80        90       100       110       120       130  |   |140       150       160       170       180       190  |      -  |    210       220       230       240       250       260       270       280       290       300       310       320       330         -  |    350       360       370       380       390       400       410       420       430       440       450       460         
                                                                                                                      133 137                                                     193       203                                                                                                                            330          343                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:415
 aligned with DPOG2_MOUSE | Q9QZM2 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                             459         
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
          DPOG2_MOUSE    40 REALVDLCRRRHFFSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPGSSQPRDSAFRLVSPESIREILQDREPSKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVSNSNQTPSSVTRVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQLAENSFARKKSLQRKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNV---------   -
               SCOP domains d1g5id2 D:40-337 The aaRS-like accessory subunit of mitochondrial polym    erase gamma, N-terminal domain                                                                                                                                                                                                 d1g5id1 D:338-468 The aaRS-like accessory subunit of mitochondrial polymerase gamma, C-terminal domain                              SCOP domains
               CATH domains 1g5iD01 D:40-353 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                      1g5iD02 D:354-468  [code=3.40.50.800, no name defined]                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eee.....ee..----.....eeehhhhhhhhhhh...hhhhhhhhhhhhhhhh.ee...hhhhhhhhhhhhhhhh.....eeeeeeeeeeee..----------.eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeee.....eeeeeeeee..eeeeeeeeeeeehhhhhhhh..hhhhh.eee..eee..eeeeeeeehhhhhhhhhhhheeeee.........eeeee..........eeeee...hhhhhhhhhhhhhhhhhh....eee.hhh....hhhhhhhhhhhh...eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g5i D  40 REALVDLCRRRHFLSGTPQQLSTAALLSGCHARFGPLGVELRKNLASQWWSSMVVFREQVFAVDSLHQEPG----RDSAFRLVSPESIREILQDREPSKEQLVAFLENLLKTSGKLRATLLHGALEHYVNCLDLVNRKLPFGLAQIGVCFHPVS----------RVGEKTEASLVWFTPTRTSSQWLDFWLRHRLLWWRKFAMSPSNFSSADCQDELGRKGSKLYYSFPWGKEPIETLWNLGDQELLHTYPGNVSTIQGRDGRKNVVPCVLSVSGDVDLGTLAYLYDSFQLAENSFARKKSLQRKVLKLHPCLAPIKVALDVGKGPTVELRQVCQGLLNELLENGISVWPGYSETVHSSLEQLHSKYDEMSVLFSVLVTETTLENGLIQLRSRDTTMKEMMHISKLRDFLVKYLASASNVAAALDHHHH 468
                                    49        59        69        79        89        99       109|    | 119       129       139       149       159       169       179       189   |     -    |  209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459         
                                                                                                110  115                                                                           193        204
   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  (2, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G5I)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DPOG2_MOUSE | Q9QZM2)
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:0004820    glycine-tRNA ligase activity    Catalysis of the reaction: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0006426    glycyl-tRNA aminoacylation    The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0032042    mitochondrial DNA metabolic process    The chemical reactions and pathways involving mitochondrial DNA.
    GO:0070584    mitochondrion morphogenesis    The process in which the anatomical structures of a mitochondrion are generated and organized.
    GO:0022904    respiratory electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:178 - Pro A:179   [ RasMol ]  
    Leu B:178 - Pro B:179   [ RasMol ]  
    Leu C:178 - Pro C:179   [ RasMol ]  
    Leu D:178 - Pro D:179   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1g5i
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    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
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DPOG2_MOUSE | Q9QZM2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DPOG2_MOUSE | Q9QZM2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DPOG2_MOUSE | Q9QZM2: 1g5h

(-) Related Entries Specified in the PDB File

1g5h MITOCHONDRIAL DNA POLYMERASE ACCESSORY SUBUNIT (SEMET VARIANT)