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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH 6-NITROINDAZOLE
 
Authors :  Z. Yin, A. J. Oakley
Date :  19 Oct 13  (Deposition) - 06 Nov 13  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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: A, B
    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  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
16NI1Ligand/Ion6-NITROINDAZOLE
2CA3Ligand/IonCALCIUM ION
3CL4Ligand/IonCHLORIDE ION
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:172 , GLY A:174 , VAL A:247 , SER A:346 , VAL A:360 , HOH A:611BINDING SITE FOR RESIDUE 6NI A 401
2AC2SOFTWAREGLY A:46 , THR A:47 , GLU A:202BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREALA A:58BINDING SITE FOR RESIDUE CL A 403
4AC4SOFTWAREGLU A:6 , HOH A:587 , ASP B:120 , HOH B:593BINDING SITE FOR RESIDUE CA A 404
5AC5SOFTWARESER A:192 , PHE A:241 , PRO A:242 , ASP A:243 , HOH A:503BINDING SITE FOR RESIDUE PEG A 406
6AC6SOFTWARETRP A:122 , GLN A:123 , SER A:124 , ARG A:224 , HOH A:539 , GLN B:36 , ALA B:38 , HOH B:510 , HOH B:532BINDING SITE FOR RESIDUE PEG A 407
7AC7SOFTWAREHIS A:226 , ILE A:231BINDING SITE FOR RESIDUE CL A 408
8AC8SOFTWARESER A:181BINDING SITE FOR RESIDUE CL A 409
9AC9SOFTWAREGLU B:6 , GLY B:85 , GLU B:87 , HOH B:680BINDING SITE FOR RESIDUE CA B 401

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:260 -A:333

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N96)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N96)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N96)

(-) Exons   (0, 0)

(no "Exon" information available for 4N96)

(-) 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4n96a1 A:1-122 DNA polymerase III, beta subunit                                                                d4n96a2 A:123-244 DNA polymerase III, beta subunit                                                                        d4n96a3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh........eeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhh......eeeeee...eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.eee...eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n96 A   1 MKFTVEREHLLKPLQQVSPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10       |29        39        49        59        69        79        89        99       109       119|      130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
                                            18|                                                                                        119|                                                                                                                                                                                                                                                     
                                             28                                                                                         121                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4n96b1 B:1-122 DNA polymerase III, beta subunit                                                                       d4n96b2 B:123-244 DNA polymerase III, beta subunit                                                                        d4n96b3 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.....hhhhhheeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeee.......eeeee.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n96 B   1 MKFTVEREHLLKPLQQVSGPLPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMR 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       254       264       274       284       294       304       314       324       334       344       354       364 
                                               21|                                                                                                                                                                                                                                252|                                                                                                               
                                                25                                                                                                                                                                                                                                 254
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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 4N96)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N96)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  4n96
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  DPO3B_ECOLI | P0A988
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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
        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 4n95 4n97 4n98 4n99 4n9a 5fku 5fkv 5fkw 5m1s

(-) Related Entries Specified in the PDB File

4n94 4n95 4n97 4n98 4n99 4n9a