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(-) Description

Title :  STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS - TRP PEPTIDE STRUCTURE
 
Authors :  V. J. Schuenemann, S. M. Kralik, R. Albrecht, S. K. Spall, K. N. Truscott D. A. Dougan, K. Zeth
Date :  03 Feb 09  (Deposition) - 28 Apr 09  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N
Biol. Unit 1:  A,H  (1x)
Biol. Unit 2:  B,I  (1x)
Biol. Unit 3:  C,J  (1x)
Biol. Unit 4:  D,K  (1x)
Biol. Unit 5:  E,L  (1x)
Biol. Unit 6:  F,M  (1x)
Biol. Unit 7:  G,N  (1x)
Keywords :  Clps, Clpa, Clpp, N-End Rule Recognition, Peptide-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. J. Schuenemann, S. M. Kralik, R. Albrecht, S. K. Spall, K. N. Truscott, D. A. Dougan, K. Zeth
Structural Basis Of N-End Rule Substrate Recognition In Escherichia Coli By The Clpap Adaptor Protein Clps.
Embo Rep. V. 10 508 2009
PubMed-ID: 19373253  |  Reference-DOI: 10.1038/EMBOR.2009.62

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
    ChainsA, B, C, D, E, F, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET
    Expression System StrainBL21(GOLD)
    Expression System Taxid511693
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainK12
    SynonymCLPS - PHE-PEPTIDE COMPLEX
 
Molecule 2 - TRP PEPTIDE
    ChainsH, I, J, K, L, M, N
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234567891011121314
Asymmetric Unit ABCDEFGHIJKLMN
Biological Unit 1 (1x)A      H      
Biological Unit 2 (1x) B      I     
Biological Unit 3 (1x)  C      J    
Biological Unit 4 (1x)   D      K   
Biological Unit 5 (1x)    E      L  
Biological Unit 6 (1x)     F      M 
Biological Unit 7 (1x)      G      N

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2WA9)

(-) Sites  (0, 0)

(no "Site" information available for 2WA9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WA9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WA9)

(-) Exons   (0, 0)

(no "Exon" information available for 2WA9)

(-) Sequences/Alignments

Asymmetric 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:83
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:83
                                                                                                          106  
                                    35        45        55        65        75        85        95       105|  
           CLPS_ECOLI    26 SMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA--   -
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa9A00 A:26-108  [code=3.30.1390.10, no name defined]                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2wa9 A  26 SMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKAGA 108
                                    35        45        55        65        75        85        95       105   

Chain B from PDB  Type:PROTEIN  Length:86
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:86
                                                                                                             106  
                                    32        42        52        62        72        82        92       102   |  
           CLPS_ECOLI    23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA--   -
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa9B00 B:23-108  [code=3.30.1390.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2wa9 B  23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKAGA 108
                                    32        42        52        62        72        82        92       102      

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:86
                                                                                                             106  
                                    32        42        52        62        72        82        92       102   |  
           CLPS_ECOLI    23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA--   -
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa9C00 C:23-108  [code=3.30.1390.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2wa9 C  23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKAGA 108
                                    32        42        52        62        72        82        92       102      

Chain D from PDB  Type:PROTEIN  Length:86
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:86
                                                                                                             106  
                                    32        42        52        62        72        82        92       102   |  
           CLPS_ECOLI    23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA--   -
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa9D00 D:23-108  [code=3.30.1390.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2wa9 D  23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKAGA 108
                                    32        42        52        62        72        82        92       102      

Chain E from PDB  Type:PROTEIN  Length:86
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:86
                                                                                                             106  
                                    32        42        52        62        72        82        92       102   |  
           CLPS_ECOLI    23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA--   -
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa9E00 E:23-108  [code=3.30.1390.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2wa9 E  23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKAGA 108
                                    32        42        52        62        72        82        92       102      

Chain F from PDB  Type:PROTEIN  Length:86
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:86
                                                                                                             106  
                                    32        42        52        62        72        82        92       102   |  
           CLPS_ECOLI    23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA--   -
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa9F00 F:23-108  [code=3.30.1390.10, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2wa9 F  23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKAGA 108
                                    32        42        52        62        72        82        92       102      

Chain G from PDB  Type:PROTEIN  Length:83
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:83
                                    33        43        53        63        73        83        93       103   
           CLPS_ECOLI    24 PPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa9G00 G:24-106  [code=3.30.1390.10, no name defined]                              CATH domains
           Pfam domains (1) ClpS-2wa9G01 G:24-103                                                           --- Pfam domains (1)
           Pfam domains (2) ClpS-2wa9G02 G:24-103                                                           --- Pfam domains (2)
           Pfam domains (3) ClpS-2wa9G03 G:24-103                                                           --- Pfam domains (3)
           Pfam domains (4) ClpS-2wa9G04 G:24-103                                                           --- Pfam domains (4)
           Pfam domains (5) ClpS-2wa9G05 G:24-103                                                           --- Pfam domains (5)
           Pfam domains (6) ClpS-2wa9G06 G:24-103                                                           --- Pfam domains (6)
           Pfam domains (7) ClpS-2wa9G07 G:24-103                                                           --- Pfam domains (7)
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2wa9 G  24 PPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    33        43        53        63        73        83        93       103   

Chain H from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2wa9 H   1 LLT   3

Chain I from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2wa9 I   1 LLT   3

Chain J from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2wa9 J   1 LLT   3

Chain K from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2wa9 K   1 LLT   3

Chain L from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2wa9 L   1 LLT   3

Chain M from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2wa9 M   1 LLT   3

Chain N from PDB  Type:PROTEIN  Length:2
                                  
               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
                 2wa9 N   1 LL   2

   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 2WA9)

(-) CATH Domains  (1, 7)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 7)

Asymmetric Unit
(-)
Family: ClpS (10)
1aClpS-2wa9G01G:24-103
1bClpS-2wa9G02G:24-103
1cClpS-2wa9G03G:24-103
1dClpS-2wa9G04G:24-103
1eClpS-2wa9G05G:24-103
1fClpS-2wa9G06G:24-103
1gClpS-2wa9G07G:24-103

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G   (CLPS_ECOLI | P0A8Q6)
molecular function
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CLPS_ECOLI | P0A8Q61lzw 1mbu 1mbv 1mbx 1mg9 1r6o 1r6q 2w9r 2wa8 3o1f 3o2b 3o2h 3o2o

(-) Related Entries Specified in the PDB File

1lzw STRUCTURAL BASIS OF CLPS-MEDIATED SWITCH IN CLPA SUBSTRATERECOGNITION
1mbu CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER
1mbv CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER TETRAGONALFORM
1mbx CRYSTAL STRUCTURE ANALYSIS OF CLPSN WITH TRANSITION METALION BOUND
1mg9 THE STRUCTURAL BASIS OF CLPS-MEDIATED SWITCH IN CLPASUBSTRATE RECOGNITION
1r6o ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA/ATP-DEPENDENT CLP PROTEASE ADAPTOR PROTEIN CLPS
1r6q CLPNS WITH FRAGMENTS
2w9r STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS
2wa8 STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS - THE PHE PEPTIDE STRUCTURE