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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH ACQLDAF
 
Authors :  Z. Yin, A. J. Oakley
Date :  11 Apr 13  (Deposition) - 01 May 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,E
Keywords :  E. Coli Sliding Clamp, 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
 
Molecule 2 - (ACE)QLDAF
    Chains: E
    Engineered: YES
    Other Details: SYNTHESIZED PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CA7Ligand/IonCALCIUM ION
3PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE3Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:86 , GLU A:87 , ALA A:89 , ARG A:100 , SER A:101 , GLY A:102 , HOH A:518 , HOH A:673BINDING SITE FOR RESIDUE PEG A 401
02AC2SOFTWARESER A:192 , GLY A:239 , PHE A:241 , HOH A:541 , HOH A:777BINDING SITE FOR RESIDUE PEG A 402
03AC3SOFTWAREGLU A:161 , GLU A:163 , ARG A:168 , TYR A:244 , ARG A:245BINDING SITE FOR RESIDUE PEG A 403
04AC4SOFTWARELYS A:250 , VAL A:344 , SER A:345 , HOH A:823 , GLU B:163 , GLU B:166 , HOH B:621 , HOH B:623BINDING SITE FOR RESIDUE PEG A 404
05AC5SOFTWAREGLY A:66 , ALA A:67 , HOH A:529 , GLU B:125BINDING SITE FOR RESIDUE CA A 405
06AC6SOFTWAREGLY A:280 , ALA A:294 , ASN A:295 , HOH A:588BINDING SITE FOR RESIDUE CA A 406
07AC7SOFTWAREHIS A:9 , ARG A:56 , VAL A:57 , ALA A:58 , ASP A:229 , HOH A:809BINDING SITE FOR RESIDUE PGE A 407
08AC8SOFTWARESER A:181BINDING SITE FOR RESIDUE CA A 408
09AC9SOFTWAREASP A:121 , TRP A:122 , ARG A:224 , HOH A:631 , HOH A:645 , ALA B:38BINDING SITE FOR RESIDUE PGE A 409
10BC1SOFTWAREGLU A:6 , GLU A:8 , GLY A:85 , GLU A:87 , HOH A:870BINDING SITE FOR RESIDUE PEG A 410
11BC2SOFTWAREASP B:211BINDING SITE FOR RESIDUE CA B 401
12BC3SOFTWAREGLY B:46 , GLU B:202BINDING SITE FOR RESIDUE CA B 402
13BC4SOFTWAREGLU B:161 , THR B:162 , SER B:190 , HIS B:191BINDING SITE FOR RESIDUE CA B 403
14BC5SOFTWAREHOH B:859 , HOH B:902BINDING SITE FOR RESIDUE CA B 404
15BC6SOFTWAREALA A:38 , HOH A:617 , HOH A:879 , ASP B:121 , TRP B:122 , ARG B:224 , HOH B:659 , HOH B:718 , HOH B:792BINDING SITE FOR RESIDUE PG4 B 405
16BC7SOFTWARETYR B:284 , LYS B:291 , HOH B:767BINDING SITE FOR RESIDUE PGE B 406
17BC8SOFTWARELYS A:74 , ASP A:77 , ALA B:271 , ILE B:272 , SER B:274 , GLU B:276 , ARG B:279 , HOH B:666 , HOH B:786BINDING SITE FOR RESIDUE PEG B 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K3Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K3Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4K3Q)

(-) 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeehhhhhhhhhhhhhhhh.....hhhhhheeeeee..eeeeeee...eeeeeeee.......eeeeehhhhhhhhhhh.......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhhh......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhh...eeeeee......eeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k3q A   1 MKFTVEREHLLKPLQQVSGLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMR 365
                                    10        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357        
                                             19|                                                                                                                                                                                                                                                                                                                                                  
                                              27                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeeeehhhhhhhhhhhhhhh.....hhhh.eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeehhhhhhhhhhh.....eeeeee...eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k3q B   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 E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4k3q E  -1 xQLDAF   4
                            |     
                           -1-ACE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (0, 0)

(no "SCOP Domain" information available for 4K3Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K3Q)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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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 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
4k3k LIGANDED SLIDING CLAMP
4k3l LIGANDED SLIDING CLAMP
4k3m LIGANDED SLIDING CLAMP
4k3o LIGANDED SLIDING CLAMP
4k3p LIGANDED SLIDING CLAMP
4k3r
4k3s