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(-) Description

Title :  DNA POLYMERASE I LARGE FRAGMENT COMPLEX 3
 
Authors :  W. Wang, L. S. Beese
Date :  08 May 12  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Dna Polymerase I, Protein-Dna Complex, Closed Form, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, H. W. Hellinga, L. S. Beese
Structures Of A High-Fidelity Dna Polymerase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A, D
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 287-878
    Gene: POLA, GK2730
    Mutation: YES
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
 
Molecule 2 - DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DNA PRIMER STRAND
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DNA TEMPLATE STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2DOC2Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION
5SUC2Ligand/IonSUCROSE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4SO4-1Ligand/IonSULFATE ION
5SUC1Ligand/IonSUCROSE
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
1CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4SO43Ligand/IonSULFATE ION
5SUC1Ligand/IonSUCROSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:629 , GLN A:656 , HIS A:682 , ARG A:702 , LYS A:706 , ALA A:707 , TYR A:710 , TYR A:714 , HOH A:1019 , HOH A:1083 , HOH A:1145 , HOH A:1174 , HOH A:1330 , DOC B:29 , DG C:3BINDING SITE FOR RESIDUE CTP A 901
2AC2SOFTWAREGLU A:325 , TYR A:327 , ASP A:372 , ARG A:375 , ASP A:408 , ILE A:605 , ASN A:607 , HOH A:1011 , HOH A:1013 , HOH A:1032 , HOH A:1053 , HOH A:1072 , HOH A:1171 , HOH A:1212 , HOH A:1223 , HOH A:1279BINDING SITE FOR RESIDUE SUC A 902
3AC3SOFTWAREGLN D:656 , GLU D:658 , HIS D:682 , ARG D:702 , LYS D:706 , TYR D:710 , TYR D:714 , ASP D:830 , MG D:902 , HOH D:1531 , HOH D:1641 , HOH D:1642 , HOH D:1643 , DOC E:29 , HOH E:203 , HOH E:228 , DG F:3 , DG F:4 , HOH F:144BINDING SITE FOR RESIDUE CTP D 901
4AC4SOFTWARECTP D:901 , HOH D:1641 , HOH D:1642 , HOH D:1643BINDING SITE FOR RESIDUE MG D 902
5AC5SOFTWARELYS D:298 , MET D:299 , ALA D:300 , ARG D:343 , ARG D:677 , HOH D:1524BINDING SITE FOR RESIDUE SO4 D 903
6AC6SOFTWAREGLU D:325 , TYR D:327 , ASP D:372 , ARG D:375 , ASP D:408 , ILE D:605 , ASN D:607 , HOH D:1009 , HOH D:1036 , HOH D:1065 , HOH D:1072 , HOH D:1089 , HOH D:1199 , HOH D:1248 , HOH D:1366 , HOH D:1508BINDING SITE FOR RESIDUE SUC D 904
7AC7SOFTWAREARG D:306 , THR D:308 , GLU D:309 , HOH D:1362BINDING SITE FOR RESIDUE SO4 D 905
8AC8SOFTWAREARG A:779 , ASN A:780 , PRO D:424 , HOH D:1490 , HOH D:1559BINDING SITE FOR RESIDUE SO4 D 906

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F2R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:620 -Pro A:621
2Glu D:620 -Pro D:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F2R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F2R)

(-) Exons   (0, 0)

(no "Exon" information available for 4F2R)

(-) 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:578
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhhh........eeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2r A 299 MAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   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       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868        


Chain B from PDB  Type:DNA  Length:9
                                         
                 4f2r B  21 CCTGACTCc  29
                                    |
                                   29-DOC


Chain C from PDB  Type:DNA  Length:11
                                           
                 4f2r C   2 TGGGAGTCAGG  12
                                    11 


Chain D from PDB  Type:PROTEIN  Length:583
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee....hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f2r D 294 KPLAKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873   


Chain E from PDB  Type:DNA  Length:9
                                         
                 4f2r E  21 CCTGACTCc  29
                                    |
                                   29-DOC


Chain F from PDB  Type:DNA  Length:12
                                            
                 4f2r F   1 ATGGGAGTCAGG  12
                                    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 4F2R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F2R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F2R)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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  4f2r
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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
        Q5KWC1_GEOKA | Q5KWC1: 2hhq 2hhs 2hht 2hvh 2hw3
UniProtKB/TrEMBL
        Q5KWC1_GEOKA | Q5KWC1: 1njw 1ua0 2hhu 2hhv 2hhw 2hhx 2hvi 3hp6 3pv8 3px0 3px4 3px6 4dqi 4dqp 4dqq 4dqr 4dqs 4ds4 4ds5 4dse 4dsf 4e0d 4ez6 4ez9 4f2s 4f3o 4f4k 4f8r

(-) Related Entries Specified in the PDB File

4ez6 4ez9 4f2s 4f3o 4f4k 4f8r