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(-) Description

Title :  CRYSTAL STRUCTURE OF ATPGS BOUND CLPX HEXAMER
 
Authors :  S. E. Glynn, A. R. Nager, B. S. Stinson, K. R. Schmitz, T. A. Baker, R. T. Sa
Date :  01 Dec 12  (Deposition) - 15 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.82
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Atpase, Hexamer, Atpgs, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Stinson, A. R. Nager, S. E. Glynn, K. R. Schmitz, T. A. Baker, R. T. Sauer
Nucleotide Binding And Conformational Switching In The Hexameric Ring Of A Aaa+ Machine.
Cell(Cambridge, Mass. ) V. 153 628 2013
PubMed-ID: 23622246  |  Reference-DOI: 10.1016/J.CELL.2013.03.029

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC
    Expression System Strain: BLR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B0438, CLPX, JW0428, LOPC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1AGS4Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:77 , VAL A:78 , ILE A:79 , GLY A:122 , SER A:123 , GLY A:124 , LYS A:125 , THR A:126 , LEU A:127 , TYR A:182 , ASP A:184 , ALA A:369BINDING SITE FOR RESIDUE AGS A 600
2AC2SOFTWARETYR B:77 , VAL B:78 , ILE B:79 , THR B:121 , GLY B:122 , SER B:123 , GLY B:124 , LYS B:125 , THR B:126 , TYR B:182 , ASP B:184 , ALA B:369BINDING SITE FOR RESIDUE AGS B 601
3AC3SOFTWAREGLY C:122 , SER C:123 , GLY C:124 , LYS C:125 , THR C:126BINDING SITE FOR RESIDUE SO4 C 500
4AC4SOFTWAREILE D:79 , THR D:121 , GLY D:122 , SER D:123 , GLY D:124 , LYS D:125 , THR D:126 , LEU D:127 , ASP D:184 , ILE D:325 , ALA D:369BINDING SITE FOR RESIDUE AGS D 501
5AC5SOFTWARETYR E:77 , VAL E:78 , ILE E:79 , GLY E:122 , SER E:123 , GLY E:124 , LYS E:125 , THR E:126 , LEU E:127 , TYR E:182 , ASP E:184 , ILE E:325 , ALA E:369BINDING SITE FOR RESIDUE AGS E 501
6AC6SOFTWAREGLY F:122 , SER F:123 , GLY F:124 , LYS F:125 , THR F:126BINDING SITE FOR RESIDUE SO4 F 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I81)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I81)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I81)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I81)

(-) Exons   (0, 0)

(no "Exon" information available for 4I81)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhhhh...eeeee.........hhhhhhhhhh...hhhhhhh.eeeeehhhhhh...hhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhh.hhhhh..hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i81 A  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTLGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSGEGVQQALLKLIEGTLQVDTSKILFICGGAFAGLDKVISHRVEEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102 ||    117       127       137       147||     162       172       182       192|      212     ||239       249       259   ||  288       298       308       318       328       338       348       358       368       378       388       398       408     
                                                                   104|                                   148|                                   192|            218|                        263|                                                                                                                                  
                                                                    110                                    154                                    203             236                         283                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee..ee.....eeee.....hhhhhhhhhhhhh...eeeee.........hhhhhhhhhh...hhhhhhh.eeeeehhhhhh...hhhhhhhhhhh.........eeee.....hhhhhhhhhhh..hhhhhhhh.hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i81 B  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKGVQQALLKLIEGTLQVDTSKILFICGGAFAGLDKVISHRVETASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102       112       122       132       142     ||157       167       177       187    || 210       237       247       257      |283       293       303       313       323       333       343       353       363       373       383       393       403       413
                                                                                                               148|                                   192|         218|                         264|                                                                                                                                    
                                                                                                                154                                    206          236                          281                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhh.eeee.hhhhh..hhhhhhh.........eeee.....hhhhhhhhhhh.hhhhhh..hhhhhhhhh.hhhhhh...eeee....hhhhhhhhh.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i81 C  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNLGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISALLKLIEGTLQVDTSKILFICGGAFAGLDKVISHRVESEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       110       120       130       140      |158       168       178       188 ||    217||     244       254       282       292       302       312       322       332       342       352       362       372       382       392       402       412 
                                                                101|                                  147|                               190|     218|                        263|                                                                                                                                   
                                                                 110                                   156                                210      236                         282                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee..ee.....eeee.....hhhhhhhhhhhhh...eeee...hhhhhhhhhh...hhhhhhh.eeee....hhhhhhhhhhhh......eeee.....hhhhhhhhhhh.hhhhhh..hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i81 D  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADDVENIIQKLLQKCDYDVQKAQRGIVYIDQIEGVQQALLKLIEGTDTSKILFICGGAFAGLDKVISHRVESEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102       112       122       132       142 ||    164       174       184 ||    212     ||242       252       262||     290       300       310       320       330       340       350       360       370       380       390       400       410   
                                                                                                           144|                          186|          218|                     263|                                                                                                                                   
                                                                                                            157                           205           239                      282                                                                                                                                   


Chain E from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhh...ee............hhhhhhhhhh...hhhhhhh.eeee.hhhhh...hhhhhhhhhhhhh.......eeee.....hhhhhhhh...hhhhhhh.hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i81 E  63 ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRGEGVQQALLKLIEGTVDTSKILFICGGAFAGLDKVISHRVSEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    72        82        92       102 ||    118       128       138       148|      163       173       183       205       215  ||   244       254       283       293       303       313       323       333       343       353       363       373       383       393       403       413
                                                                   104|                                  148|                                  191|           218|                     262|                                                                                                                                   
                                                                    111                                   154                                   204            238                      282                                                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..........eeee.....hhhhhhhhhhhhh...eeeee......hhhhhhhhhh...hhhhhhh.eeeeehhhhhh...hhhhhhhhhhh.......eeee.....hhhhhhhhhhh.hhhhhhh..hhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.......eeeehhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i81 F  64 LPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSLGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKGVQQALLKLIEGTVDTSKILFICGGAFAGLDKVISHRVEASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIY 413
                                    73        83        93       103 ||    117       127       137       147|      165       175       185      |208       218|      247       257     ||284       294       304       314       324       334       344       354       364       374       384       394       404         
                                                                   105|                                  147|                                 192|         218|                      263|                                                                                                                                    
                                                                    110                                   156                                  206          238                       281
   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 4I81)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I81)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I81)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  4i81
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  CLPX_ECOLI | P0A6H1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CLPX_ECOLI | P0A6H1: 1ovx 2ds5 2ds6 2ds7 2ds8 3hte 3hws 4i34 4i4l 4i5o 4i63 4i9k

(-) Related Entries Specified in the PDB File

3hte 3hws 4i34 4i4l 4i5o 4i63 4i8v