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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH 5-CHLOROINDOLINE-2,3-DIONE
 
Authors :  Z. Yin, A. J. Oakley
Date :  19 Oct 13  (Deposition) - 06 Nov 13  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sliding Clamp, Dnan, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yin, L. R. Whittell, Y. Wang, S. Jergic, M. Liu, E. J. Harry, N. E. Dixon, J. L. Beck, M. J. Kelso, A. J. Oakley
Discovery Of Lead Compounds Targeting The Bacterial Sliding Clamp Using A Fragment-Based Approach.
J. Med. Chem. V. 57 2799 2014
PubMed-ID: 24592885  |  Reference-DOI: 10.1021/JM500122R

(-) Compounds

Molecule 1 - DNA POLYMERASE III SUBUNIT BETA
    Chains: B, A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PND261
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B3701, DNAN, JW3678
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: BETA SLIDING CLAMP, BETA CLAMP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
12HQ1Ligand/Ion5-CHLORO-1H-INDOLE-2,3-DIONE
2CA4Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:121 , TRP A:122 , GLN A:123 , SER A:124 , GLN A:217 , ARG A:224 , HOH A:644 , VAL B:37 , ALA B:38 , GLY B:66BINDING SITE FOR RESIDUE PG4 B 401
02AC2SOFTWARESER B:18 , LEU B:21 , ARG B:73 , PHE B:76 , ARG B:80 , HOH B:746BINDING SITE FOR RESIDUE PG4 B 402
03AC3SOFTWAREHOH A:691 , ASP B:121 , TRP B:122 , GLN B:123 , SER B:124 , GLN B:217 , ARG B:224 , HOH B:546BINDING SITE FOR RESIDUE PEG B 403
04AC4SOFTWAREGLU B:87 , ALA B:89 , ARG B:100 , SER B:101 , GLY B:102 , GLU B:287 , HOH B:760BINDING SITE FOR RESIDUE PEG B 404
05AC5SOFTWARETHR A:172 , GLY A:174 , HIS A:175 , ARG A:176 , VAL A:247 , VAL A:360BINDING SITE FOR RESIDUE 2HQ A 401
06AC6SOFTWARESER A:181 , GLU A:350 , GLN A:355 , SER A:356BINDING SITE FOR RESIDUE PEG A 402
07AC7SOFTWAREMET A:1 , GLU A:64 , PRO A:65 , ALA A:67 , GLU B:125BINDING SITE FOR RESIDUE PEG A 403
08AC8SOFTWAREARG A:105 , TYR A:284 , VAL A:285 , GLU A:314 , MET A:315 , GLU B:303 , ILE B:305BINDING SITE FOR RESIDUE PEG A 404
09AC9SOFTWAREALA A:58BINDING SITE FOR RESIDUE CL A 405
10BC1SOFTWAREARG A:246 , LEU A:248 , LYS A:250 , SER A:346 , HOH A:561BINDING SITE FOR RESIDUE PGE A 406
11BC2SOFTWAREGLU A:95 , THR A:110 , HOH A:643 , HOH A:708BINDING SITE FOR RESIDUE CA A 407
12BC3SOFTWAREASN A:32 , PRO A:71 , SER A:109 , THR A:110 , LEU A:111 , GLU B:334BINDING SITE FOR RESIDUE CA A 408
13BC4SOFTWAREHIS A:226BINDING SITE FOR RESIDUE CA A 409
14BC5SOFTWAREGLY A:85 , GLU A:87 , HOH A:711 , ASP B:120BINDING SITE FOR RESIDUE CA A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N95)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N95)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N95)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N95)

(-) Exons   (0, 0)

(no "Exon" information available for 4N95)

(-) 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 d4n95a1 A:1-122 DNA polymerase III, beta subunit                                                                    d4n95a2 A:123-244 DNA polymerase III, beta subunit                                                                        d4n95a3 A:245-365 DNA polymerase III, beta subunit                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhh..hhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.......eeeeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.....eeeeeee..eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.eee...eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n95 A   1 MKFTVEREHLLKPLQQVSGPLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMR 365
                                    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         
                                               21|                                                                                                                                                                                                                                                                                                                                                 
                                                28                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4n95b1 B:1-122 DNA polymerase III, beta subunit                                                                       d4n95b2 B:123-244 DNA polymerase III, beta subunit                                                                        d4n95b3 B:245-365 DNA polymerase III, beta subunit                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhh.....hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n95 B   1 MKFTVEREHLLKPLQQVSGPLPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMR 365
                                    10        20||      33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363  
                                               21|                                                                                                                                                                                                                                                                                                                                                    
                                                25
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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 4N95)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N95)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO3B_ECOLI | P0A988: 1jqj 1jql 1mmi 1ok7 1unn 1wai 2pol 2xur 3bep 3d1e 3d1f 3d1g 3f1v 3pwe 3q4j 3q4k 3q4l 3qsb 4k3k 4k3l 4k3m 4k3o 4k3p 4k3q 4k3r 4k3s 4mjp 4mjq 4mjr 4n94 4n96 4n97 4n98 4n99 4n9a 5fku 5fkv 5fkw 5m1s

(-) Related Entries Specified in the PDB File

4n94 4n96 4n97 4n98 4n99 4n9a