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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH (S)-2-(4-METHYLPENTANAMIDO)-3-PHENYLPROPANOIC ACID
 
Authors :  Z. Yin, A. J. Oakley
Date :  10 Apr 13  (Deposition) - 01 May 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Poliii Beta, Sliding Clamp, Dnan, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yin, M. J. Kelso, J. L. Beck, A. J. Oakley
Structural And Thermodynamic Dissection Of Linear Motif Recognition By The E. Coli Sliding Clamp
J. Med. Chem. V. 56 8665 2013
PubMed-ID: 24090409  |  Reference-DOI: 10.1021/JM401118F

(-) 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: DNAN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG44Ligand/IonTETRAETHYLENE GLYCOL
5SFK1Ligand/IonN-(4-METHYLPENTANOYL)-L-PHENYLALANINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:6 , GLN A:61 , HOH A:685 , HOH B:596BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWAREGLU A:161 , HOH A:642 , HOH A:798BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREGLY A:46 , HOH A:723BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWARESER A:181 , GLN A:355 , HOH A:760 , ARG B:365BINDING SITE FOR RESIDUE PG4 A 404
05AC5SOFTWAREGLN A:123 , SER A:124 , GLN A:217 , HOH A:669 , GLN B:36 , VAL B:37 , ALA B:38 , ASP B:39 , GLY B:66 , HOH B:604BINDING SITE FOR RESIDUE PG4 A 405
06AC6SOFTWAREMET A:1 , PRO A:65 , GLY A:66 , ALA A:67 , LEU A:92 , GLN B:123 , GLU B:125 , HOH B:581 , HOH B:668BINDING SITE FOR RESIDUE PEG A 406
07AC7SOFTWARETHR A:172 , GLY A:174 , HIS A:175 , ARG A:176 , PRO A:242 , MET A:362 , HOH A:552 , HOH A:557 , HOH A:573 , HOH A:590 , HOH A:601 , HOH A:738 , HOH B:560BINDING SITE FOR RESIDUE SFK A 407
08AC8SOFTWAREHOH A:572 , GLU B:6 , GLY B:85 , GLU B:87 , HOH B:804 , HOH B:805BINDING SITE FOR RESIDUE CA B 401
09AC9SOFTWARESER B:18 , LEU B:21 , ARG B:73 , PHE B:76 , ARG B:80 , HOH B:632 , HOH B:798BINDING SITE FOR RESIDUE PG4 B 402
10BC1SOFTWAREVAL A:151 , ARG A:152 , GLN A:265 , ARG B:7 , ARG B:80 , GLY B:81 , LEU B:82 , HOH B:589BINDING SITE FOR RESIDUE PG4 B 403
11BC2SOFTWAREHOH A:550 , VAL B:5 , GLU B:6 , HIS B:9 , GLN B:61 , HOH B:520BINDING SITE FOR RESIDUE CL B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K3K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K3K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K3K)

(-) Exons   (0, 0)

(no "Exon" information available for 4K3K)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4k3ka1 A:1-122 DNA polymerase III, beta subunit                                                                  d4k3ka2 A:123-244 DNA polymerase III, beta subunit                                                                        d4k3ka3 A:245-366 DNA polymerase III, beta subunit                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.......eeeeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeehhhhhhhhhh......eeeeeee..eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.ee....eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k3k A   1 MKFTVEREHLLKPLQQVSLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    10       |28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358        
                                            18|                                                                                                                                                                                                                                                                                                                                                   
                                             27                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4k3kb1 B:1-122 DNA polymerase III, beta subunit                                                                          d4k3kb2 B:123-244 DNA polymerase III, beta subunit                                                                        d4k3kb3 B: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..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhhhheeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.ee....eeeeeehhhhhhhhhhhh..eeeeee......eeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k3k B   1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL 366
                                    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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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4K3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K3K)

(-) 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 4k3l 4k3m 4k3o 4k3p 4k3q 4k3r 4k3s 4mjp 4mjq 4mjr 4n94 4n95 4n96 4n97 4n98 4n99 4n9a 5fku 5fkv 5fkw 5m1s

(-) Related Entries Specified in the PDB File

1mmi NATIVE STRUCTURE IN P21 SPACE GROUP
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