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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH 6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-7-CARBOXYLIC ACID
 
Authors :  Z. Yin, A. J. Oakley
Date :  19 Oct 13  (Deposition) - 06 Nov 13  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Poliii Beta, Sliding Clamp, Dnan, Transferase-Transferase Inhibitor Complex (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 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, 35)

Asymmetric/Biological Unit (4, 35)
No.NameCountTypeFull Name
12J11Ligand/Ion6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-7-CARBOXYLICACID
2CA5Ligand/IonCALCIUM ION
3PEG19Ligand/IonDI(HYDROXYETHYL)ETHER
4PG410Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:152 , GLY A:174 , PRO A:242 , VAL A:247 , SER A:346 , MET A:362 , HOH A:523BINDING SITE FOR RESIDUE 2J1 A 401
02AC2SOFTWAREARG A:103 , SER A:286 , GLU A:287 , GLN A:289 , PG4 A:416BINDING SITE FOR RESIDUE PEG A 402
03AC3SOFTWARETRP A:122 , GLN A:217 , ARG A:224 , HOH A:520 , ALA B:38BINDING SITE FOR RESIDUE PEG A 403
04AC4SOFTWAREALA A:268 , ARG A:279 , LEU A:325 , ASP B:77 , ARG B:80 , GLY B:81BINDING SITE FOR RESIDUE PG4 A 404
05AC5SOFTWAREGLN A:36 , SER A:43 , ARG A:56 , ILE A:231BINDING SITE FOR RESIDUE PEG A 405
06AC6SOFTWAREARG A:80 , GLY A:81 , PRO A:83 , GLN B:265BINDING SITE FOR RESIDUE PEG A 406
07AC7SOFTWAREALA A:58BINDING SITE FOR RESIDUE CA A 407
08AC8SOFTWARESER A:181 , GLN A:348 , GLN A:355 , SER A:356 , HOH A:548BINDING SITE FOR RESIDUE PEG A 408
09AC9SOFTWAREGLU A:316 , LEU A:366BINDING SITE FOR RESIDUE CA A 409
10BC1SOFTWAREPRO A:83 , GLY A:102 , ARG A:103 , SER A:104 , PG4 A:415 , HOH A:583 , ARG B:269BINDING SITE FOR RESIDUE PG4 A 410
11BC2SOFTWAREASP A:229BINDING SITE FOR RESIDUE CA A 411
12BC3SOFTWARELEU A:262 , ALA A:266 , ARG A:269 , ILE A:305 , LEU A:306 , ASP A:307 , HOH A:565 , PG4 B:401 , PEG B:415BINDING SITE FOR RESIDUE PEG A 412
13BC4SOFTWAREGLU A:64 , PRO B:189BINDING SITE FOR RESIDUE PEG A 413
14BC5SOFTWAREGLN A:299 , GLU A:301 , SER B:107 , TYR B:284 , PG4 B:412BINDING SITE FOR RESIDUE PEG A 414
15BC6SOFTWAREPRO A:112 , ALA A:114 , ASP A:115 , PG4 A:410 , ILE B:305 , LEU B:306BINDING SITE FOR RESIDUE PG4 A 415
16BC7SOFTWAREARG A:105 , GLN A:289 , PEG A:402 , HOH A:596 , ILE B:305 , PG4 B:412BINDING SITE FOR RESIDUE PG4 A 416
17BC8SOFTWAREGLU A:314BINDING SITE FOR RESIDUE CA A 417
18BC9SOFTWAREARG A:137BINDING SITE FOR RESIDUE PEG A 418
19CC1SOFTWARELEU A:262 , ARG A:269 , PEG A:412 , HOH A:599 , PRO B:83 , PEG B:415 , HOH B:513BINDING SITE FOR RESIDUE PG4 B 401
20CC2SOFTWARESER B:18 , ARG B:73 , PHE B:76 , ARG B:80 , PEG B:416 , HOH B:551 , HOH B:576BINDING SITE FOR RESIDUE PG4 B 402
21CC3SOFTWAREGLU B:52 , ARG B:56 , ASN B:118 , LEU B:119 , HOH B:555BINDING SITE FOR RESIDUE PEG B 403
22CC4SOFTWAREARG A:152 , ARG B:7 , ARG B:80 , LEU B:82 , HOH B:580BINDING SITE FOR RESIDUE PG4 B 404
23CC5SOFTWAREALA A:38 , ARG B:215 , GLN B:217 , ARG B:224 , HIS B:226 , ILE B:231 , PEG B:413BINDING SITE FOR RESIDUE PEG B 405
24CC6SOFTWARELYS B:264 , GLN B:265 , ALA B:268 , ALA B:271 , ARG B:279 , LEU B:325 , ASN B:329BINDING SITE FOR RESIDUE PG4 B 406
25CC7SOFTWAREASP B:229BINDING SITE FOR RESIDUE PEG B 407
26CC8SOFTWAREGLU B:50 , TYR B:153 , ASN B:156 , GLY B:157 , PRO B:196 , ARG B:197BINDING SITE FOR RESIDUE PEG B 408
27CC9SOFTWAREGLU A:276 , ARG B:73 , LYS B:74 , PEG B:416BINDING SITE FOR RESIDUE PEG B 410
28DC1SOFTWAREGLN A:123 , GLU A:125 , ALA B:67 , GLY B:94 , PRO B:112 , ALA B:113 , ALA B:114BINDING SITE FOR RESIDUE PG4 B 411
29DC2SOFTWAREGLU A:301 , GLU A:303 , PEG A:414 , PG4 A:416 , ARG B:105 , SER B:107 , TYR B:284 , SER B:286BINDING SITE FOR RESIDUE PG4 B 412
30DC3SOFTWAREASP B:121 , TRP B:122 , SER B:124 , ARG B:224 , PEG B:405BINDING SITE FOR RESIDUE PEG B 413
31DC4SOFTWARESER B:181 , GLN B:348 , GLN B:355 , SER B:356 , HOH B:603BINDING SITE FOR RESIDUE PEG B 414
32DC5SOFTWAREARG A:269 , ILE A:305 , PEG A:412 , LEU B:82 , PRO B:83 , ALA B:86 , SER B:101 , ARG B:103 , SER B:104 , PG4 B:401 , HOH B:600BINDING SITE FOR RESIDUE PEG B 415
33DC6SOFTWAREPRO B:25 , ARG B:73 , PG4 B:402 , PEG B:410BINDING SITE FOR RESIDUE PEG B 416
34DC7SOFTWAREGLU B:93 , SER B:107BINDING SITE FOR RESIDUE CA B 417

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N99)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N99)

(-) Exons   (0, 0)

(no "Exon" information available for 4N99)

(-) 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 d4n99a1 A:1-122 DNA polymerase III, beta subunit                                                                    d4n99a2 A:123-244 DNA polymerase III, beta subunit                                                                    d4n99a3 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...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee.ee.hhh.......eeeeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhh..eeeeeee..eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n99 A   1 MKFTVEREHLLKPLQQVSGPLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206||     220       230       240       250       260       270       280       290       300       310       320       330       340       350       360      
                                              20|                                                                                                                                                                                 207|                                                                                                                                                          
                                               27                                                                                                                                                                                  212                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4n99b1 B:1-122 DNA polymerase III, beta subunit                                                                         d4n99b2 B:123-244 DNA polymerase III, beta subunit                                                                        d4n99b3 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.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n99 B   1 MKFTVEREHLLKPLQQVSGPLGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10        20||      31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361     
                                               21|                                                                                                                                                                                                                                                                                                                                                       
                                                23
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  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 4N99)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N99)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

4n94 4n95 4n96 4n97 4n98 4n9a