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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH (R)-6-BROMO-9-(2-((S)-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 :  2.00
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, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
12VM2Ligand/Ion(2R)-6-BROMO-9-(2-{[(1S)-1-CARBOXY-2-PHENYLETHYL]AMINO}-2-OXOETHYL)-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-2-CARBOXYLIC ACID
2CA4Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:152 , TYR A:154 , THR A:172 , GLY A:174 , HIS A:175 , ARG A:176 , PRO A:242 , VAL A:247 , MET A:362 , HOH A:790BINDING SITE FOR RESIDUE 2VM A 401
02AC2SOFTWAREASN A:118 , LEU A:119 , HOH A:525 , HOH A:555 , HOH A:557 , HOH A:599 , HOH B:559BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWARESER A:181 , SER A:356BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWARELEU B:262 , ALA B:266 , ARG B:269 , HOH B:532 , HOH B:616BINDING SITE FOR RESIDUE CL B 401
05AC5SOFTWARETYR B:153 , TYR B:154 , THR B:172 , ASP B:173 , GLY B:174 , HIS B:175 , ARG B:176 , MET B:362 , HOH B:790BINDING SITE FOR RESIDUE 2VM B 402
06AC6SOFTWAREASN B:118 , LEU B:119 , HOH B:535 , HOH B:553 , HOH B:582 , HOH B:627 , HOH B:644BINDING SITE FOR RESIDUE CA B 403
07AC7SOFTWARESER B:181 , SER B:356BINDING SITE FOR RESIDUE CA B 404
08AC8SOFTWAREARG B:7 , ARG B:80 , LEU B:82 , GLU B:84BINDING SITE FOR RESIDUE PEG B 405
09AC9SOFTWAREGLU A:303 , TYR B:284 , SER B:286 , GLN B:289 , LYS B:291BINDING SITE FOR RESIDUE PEG B 406
10BC1SOFTWARELYS B:2 , VAL B:90 , GLN B:91 , GLU B:93 , LEU B:98 , ARG B:100 , ALA B:313 , GLU B:314 , HOH B:623 , HOH B:762BINDING SITE FOR RESIDUE PEG B 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly B:19 -Pro B:20
2Pro B:20 -Leu B:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PNW)

(-) 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4pnwa1 A:1-122 DNA polymerase III, beta subunit                                                                          d4pnwa2 A:123-244 DNA polymerase III, beta subunit                                                                        d4pnwa3 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.........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
                 4pnw A   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPM 364
                                    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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4pnwb1 B:1-122 DNA polymerase III, beta subunit                                                                          d4pnwb2 B:123-244 DNA polymerase III, beta subunit                                                                        d4pnwb3 B:245-364 DNA polymerase III, beta subunit                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhh........hhhh.eeeeeee..eeeeeee....eeeeeee....ee.eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh..........eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pnw B   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPM 364
                                    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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  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 4PNW)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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(-) Related Entries Specified in the PDB File

4ovf 4ovg 4ovh 4pnu 4pnv