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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH (R)-6-BROMO-9-(2-((R)-1-CARBOXY-2-PHENYLETHYLAMINO)-2-OXOETHYL)-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-2-CARBOXYLIC ACID
 
Authors :  Z. Yin, A. J. Oakley
Date :  21 Feb 14  (Deposition) - 05 Mar 14  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Poliii Beta, Sliding Clamp, Dnan, Transferase, Transferase- Transferase Inhibitor Complex (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  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
12VD2Ligand/Ion(2R)-6-BROMO-9-(2-{[(1R)-1-CARBOXY-2-PHENYLETHYL]AMINO}-2-OXOETHYL)-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-2-CARBOXYLIC ACID
2CA2Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4PEG5Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:344 , SER A:345 , HOH A:552 , HOH A:587 , HOH A:659 , HOH A:742 , GLU B:163 , GLU B:166 , HOH B:696BINDING SITE FOR RESIDUE PEG A 401
02AC2SOFTWAREASP A:121 , TRP A:122 , ARG A:224 , HOH A:557 , HOH A:763 , HOH B:678BINDING SITE FOR RESIDUE PEG A 402
03AC3SOFTWAREGLU A:161 , GLU A:163 , ARG A:168 , ASP A:243 , TYR A:244 , ARG A:245 , HOH A:555 , HOH A:721 , HOH A:790BINDING SITE FOR RESIDUE PEG A 403
04AC4SOFTWAREGLU A:334 , HOH A:716 , HOH A:812 , HOH A:851BINDING SITE FOR RESIDUE CA A 404
05AC5SOFTWAREARG A:152 , TYR A:154 , THR A:172 , GLY A:174 , ARG A:176 , VAL A:247 , VAL A:360 , MET A:362 , HOH A:830 , LYS B:250 , ASN B:251BINDING SITE FOR RESIDUE 2VD A 405
06AC6SOFTWARESER A:181 , SER A:356BINDING SITE FOR RESIDUE CA A 406
07AC7SOFTWAREALA A:38 , HOH A:726 , HOH A:857 , TRP B:122 , ARG B:224 , HOH B:575 , HOH B:585BINDING SITE FOR RESIDUE PEG B 401
08AC8SOFTWAREGLN A:265 , ARG B:7 , ARG B:80 , GLY B:81 , LEU B:82 , HOH B:591BINDING SITE FOR RESIDUE PEG B 402
09AC9SOFTWARELEU B:262 , ALA B:266 , ARG B:269 , HOH B:531 , HOH B:577BINDING SITE FOR RESIDUE CL B 403
10BC1SOFTWAREARG B:152 , TYR B:154 , GLY B:174 , ARG B:176 , LEU B:177BINDING SITE FOR RESIDUE 2VD B 404
11BC2SOFTWAREARG B:282 , THR B:293 , ASN B:295 , HOH B:512BINDING SITE FOR RESIDUE CL B 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PNU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PNU)

(-) 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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4pnua1 A:1-122 DNA polymerase III, beta subunit                                                                     d4pnua2 A:123-244 DNA polymerase III, beta subunit                                                                        d4pnua3 A:245-364 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.........eeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhh......eeeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhhh......eeeeeee..eeeeeee.....eeeeeee.ee....eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pnu A   1 MKFTVEREHLLKPLQQVSGPLLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPM 364
                                    10        20||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355         
                                               21|                                                                                                                                                                                                                                                                                                                                                 
                                                27                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4pnub1 B:1-122 DNA polymerase III, beta subunit                                                                    d4pnub2 B:123-244 DNA polymerase III, beta subunit                                                                        d4pnub3 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.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhhh......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pnu B   1 MKFTVEREHLLKPLQQVSGPLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
                                              20|                                                                                                                                                                                                                                                                                                                                                   
                                               27
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  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 4PNU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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(-) Related Entries Specified in the PDB File

4ovf 4ovg 4ovh 4pnv 4pnw