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(-) Description

Title :  E. COLI SLIDING CLAMP APO-CRYSTAL IN P21 SPACE GROUP WITH LARGER CELL DIMENSIONS
 
Authors :  Z. Yin, A. J. Oakley
Date :  21 Feb 14  (Deposition) - 05 Mar 14  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Poliii Beta, Sliding Clamp, Dnan, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yin, L. R. Whittell, Y. Wang, S. Jergic, C. Ma, P. J. Lewis, N. E. Dixon J. L. Beck, M. J. Kelso, A. J. Oakley
Bacterial Sliding Clamp Inhibitors That Mimic The Sequentia Binding Mechanism Of Endogenous Linear Motifs.
J. Med. Chem. V. 58 4693 2015
PubMed-ID: 25970224  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00232

(-) Compounds

Molecule 1 - DNA POLYMERASE III SUBUNIT BETA
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PND261
    Expression System Strain: AN1459
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BN896_3391, DNAN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 1403831
    Strain: K-12 SUBSTR. MC4100

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:118 , LEU A:119 , HOH A:520 , HOH A:542 , HOH A:543 , HOH A:581 , HOH A:643BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWAREGLU A:6 , HIS A:9 , GLN A:61 , HOH A:579 , HOH A:891BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWAREARG A:103 , ARG A:105 , GLU B:303 , ILE B:305BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWAREVAL A:17 , SER A:18 , LEU A:30 , GLY A:31 , GLY A:46 , MET A:53 , ALA A:72 , HOH A:922BINDING SITE FOR RESIDUE PEG A 404
05AC5SOFTWARETYR A:153 , VAL A:237 , HOH A:515 , HOH A:746BINDING SITE FOR RESIDUE CA A 405
06AC6SOFTWAREHIS A:255 , SER A:311 , GLY A:312 , HOH A:745 , HOH A:889 , HOH A:893BINDING SITE FOR RESIDUE CA A 406
07AC7SOFTWARELEU A:14 , SER A:18 , LEU A:33 , HOH A:725BINDING SITE FOR RESIDUE CA A 407
08AC8SOFTWAREASN B:118 , LEU B:119 , HOH B:520 , HOH B:522 , HOH B:557 , HOH B:596 , HOH B:661BINDING SITE FOR RESIDUE CA B 401
09AC9SOFTWAREGLU A:125 , HOH A:871 , MET B:1 , PRO B:65 , GLY B:66 , ALA B:67 , LEU B:92 , HOH B:727 , HOH B:923BINDING SITE FOR RESIDUE PEG B 402
10BC1SOFTWAREGLN A:123 , HOH A:516 , HOH A:695 , GLN B:36 , ALA B:38 , THR B:41 , LEU B:42 , SER B:43BINDING SITE FOR RESIDUE PEG B 403
11BC2SOFTWARETHR B:4 , VAL B:5 , LEU B:59 , VAL B:60 , GLN B:61 , HOH B:503 , HOH B:642BINDING SITE FOR RESIDUE CA B 404
12BC3SOFTWARETHR B:110 , LEU B:111 , PRO B:112 , HOH B:507 , HOH B:911BINDING SITE FOR RESIDUE CA B 405
13BC4SOFTWAREHOH A:561 , HOH A:781 , GLN B:265 , ARG B:269 , HOH B:517BINDING SITE FOR RESIDUE CL B 406
14BC5SOFTWAREARG B:105 , SER B:286 , GLU B:287 , HOH B:595 , HOH B:786BINDING SITE FOR RESIDUE CL B 407
15BC6SOFTWAREGLN B:16 , ARG B:205 , PHE B:230 , HOH B:706 , HOH B:958BINDING SITE FOR RESIDUE CL B 408

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:23 -Arg A:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PNV)

(-) Sequences/Alignments

Asymmetric/Biological 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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4pnva1 A:1-122 DNA polymerase III, beta subunit                                                                          d4pnva2 A:123-244 DNA polymerase III, beta subunit                                                                        d4pnva3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhh........hhhh.eeeeeee..eeeeeee....eeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhhhheeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhh...eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pnv A   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        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      


Chain B from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4pnvb1 B:1-122 DNA polymerase III, beta subunit                                                                          d4pnvb2 B:123-244 DNA polymerase III, beta subunit                                                                        d4pnvb3 B:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh.......hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhhhheeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pnv B   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20        30        40        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
   Legend:   → Mismatch (orange background)
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    → 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  (1, 6)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PNV)

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

4ovf 4ovg 4ovh 4pnu 4pnw