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(-) Description

Title :  E. COLI SLIDING CLAMP IN COMPLEX WITH ACLF DIPEPTIDE
 
Authors :  Z. Yin, A. J. Oakley
Date :  10 Apr 13  (Deposition) - 01 May 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  E. Coli 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  (8, 26)

Asymmetric/Biological Unit (8, 26)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CA12Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5LEU2Mod. Amino AcidLEUCINE
6PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
7PGE1Ligand/IonTRIETHYLENE GLYCOL
8PHE2Mod. Amino AcidPHENYLALANINE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:6 , HIS A:9 , GLN A:61 , HOH A:560BINDING SITE FOR RESIDUE CA A 403
02AC2SOFTWARESER A:181 , GLN A:355 , SER A:356BINDING SITE FOR RESIDUE CA A 404
03AC3SOFTWAREASN A:275 , ARG A:282 , ASN A:295 , ASN A:296 , PRO A:297 , HOH A:535BINDING SITE FOR RESIDUE PEG A 405
04AC4SOFTWAREASP A:121 , TRP A:122 , ARG A:224 , HOH A:828BINDING SITE FOR RESIDUE PEG A 406
05AC5SOFTWAREHOH A:618 , HOH A:859 , MET B:1 , LYS B:2 , GLU B:64BINDING SITE FOR RESIDUE CA A 408
06AC6SOFTWAREHOH A:534 , GLU B:163 , GLU B:166 , HOH B:588 , HOH B:617 , HOH B:792BINDING SITE FOR RESIDUE CA B 403
07AC7SOFTWAREPRO B:249 , PRO B:252 , MET B:339 , LEU B:340 , THR B:341 , SER B:346BINDING SITE FOR RESIDUE CA B 404
08AC8SOFTWAREGLY B:46 , GLU B:202BINDING SITE FOR RESIDUE CA B 406
09AC9SOFTWAREASP B:121 , TRP B:122 , ARG B:224 , HOH B:651 , HOH B:836BINDING SITE FOR RESIDUE PEG B 407
10BC1SOFTWAREALA B:133 , HOH B:868BINDING SITE FOR RESIDUE PEG B 408
11BC2SOFTWAREGLN B:132 , MET B:206 , ASP B:208 , GLY B:210 , ASP B:211 , ASN B:212 , VAL B:227 , PHE B:230 , HOH B:615 , HOH B:805 , HOH B:806BINDING SITE FOR RESIDUE PGE B 409
12BC3SOFTWARESER B:187 , LEU B:188 , PRO B:189 , HOH B:786 , HOH B:818BINDING SITE FOR RESIDUE PEG B 410
13BC4SOFTWAREPRO A:65 , VAL B:126 , GLU B:127 , HOH B:616 , HOH B:790BINDING SITE FOR RESIDUE CA B 412
14BC5SOFTWAREPRO B:83 , HOH B:656BINDING SITE FOR RESIDUE CA B 413
15BC6SOFTWAREGLU B:161 , GLU B:163 , ARG B:168 , ASP B:243 , TYR B:244 , ARG B:245 , HOH B:648BINDING SITE FOR RESIDUE EDO B 414
16BC7SOFTWAREGLU B:95 , THR B:110 , HOH B:688 , HOH B:817 , HOH B:822BINDING SITE FOR RESIDUE CL B 416
17BC8SOFTWAREHOH A:724 , HOH A:758 , HOH B:685 , HOH B:691 , HOH B:767 , HOH B:899BINDING SITE FOR RESIDUE CA B 417
18BC9SOFTWAREARG A:152 , THR A:172 , GLY A:174 , ARG A:176 , PRO A:242 , MET A:362 , HOH A:563 , HOH A:611 , HOH A:652 , ASN B:251BINDING SITE FOR LINKED RESIDUES A 400 to 402
19CC1SOFTWARETHR B:172 , GLY B:174 , HIS B:175 , ARG B:176 , PRO B:242 , MET B:362 , HOH B:599 , HOH B:759BINDING SITE FOR LINKED RESIDUES B 400 to 402

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:260 -A:333
2B:260 -B:333

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K3L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K3L)

(-) Exons   (0, 0)

(no "Exon" information available for 4K3L)

(-) 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 d4k3la1 A:1-122 DNA polymerase III, beta subunit                                                                 d4k3la2 A:123-244 DNA polymerase III, beta subunit                                                                     d4k3la3 A:245-365 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.....hhhhhheeeeee..eeeeeee...eeeeeeee.......eeeeehhhhhhhhhhh...eeeeee...eeeeee..eeeeee.......hhhhh......eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k3l A   1 MKFTVEREHLLKPLQQVSPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRxLF 402
                                    10       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362  ||  
                                            18|                                                                                                                                                                                 208|                                                                                                                                                      365|  
                                             28                                                                                                                                                                                  212                                                                                                                                                       400-ACE


Chain B from PDB  Type:PROTEIN  Length:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4k3lb1 B:1-122 DNA polymerase III, beta subunit                                                                   d4k3lb2 B:123-244 DNA polymerase III, beta subunit                                                                        d4k3lb3 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.....hhhh.eeeeeee..eeeeeee...eeeeeeee.......eeeeeehhhhhhhhhhh......eeeee...eeeeee..eeeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh.......eeeeeee..eeeeeee.....eeeeeee.......eeeeeehhhhhhhhhhhh..eeeeee......eeeee..eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k3l B   1 MKFTVEREHLLKPLQQVSGLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRLxLF 402
                                    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       400  
                                             19|                                                                                                                                                                                                                                                                                                                                                366|  
                                              27                                                                                                                                                                                                                                                                                                                                                 400-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  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K3L)

(-) 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 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

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