Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF E. COLI DNAK IN COMPLEX WITH A SHORT PYRRHOCORICIN-DERIVED INHIBITOR PEPTIDE
 
Authors :  A. Roujeinikova
Date :  09 Jul 08  (Deposition) - 10 Mar 09  (Release) - 10 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 2:  A,D  (1x)
Biol. Unit 3:  B,C  (1x)
Keywords :  Molecular Chaperone, Dnak, Hsp70, Substrate-Binding Domain, Pyrrhocoricin Inhibitor, Atp-Binding, Chaperone, Cytoplasm, Dna Replication, Membrane, Nucleotide-Binding, Phosphoprotein, Stress Response, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Liebscher, A. Roujeinikova
Allosteric Coupling Between The Lid And Interdomain Linker In Dnak Revealed By Inhibitor Binding Studies
J. Bacteriol. V. 191 1456 2009
PubMed-ID: 19103929  |  Reference-DOI: 10.1128/JB.01131-08
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN DNAK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: SUBSTRATE BINDING DOMAIN (UNP RESIDUES 389 TO 607)
    Gene: DNAK, GROP, GRPF, SEG, B0014, JW0013
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Synonym: HEAT SHOCK PROTEIN 70, HEAT SHOCK 70 KDA PROTEIN, HSP70
 
Molecule 2 - INHIBITOR PEPTIDE
    Chains: C, D
    Engineered: YES
    Other Details: THE PEPTIDE WAS PYRRHOCORICIN-DERIVED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 2 (1x): A  D
Biological Unit 3 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ALC2Mod. Amino Acid2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ALC1Mod. Amino Acid2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ALC1Mod. Amino Acid2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1ALC1Mod. Amino Acid2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:402 , MET A:404 , GLY A:405 , GLY A:406 , HOH A:1104 , HOH A:1208 , HOH A:1228 , PRO D:5BINDING SITE FOR RESIDUE SO4 A 1002
2AC2SOFTWAREASN A:451 , LYS A:452 , SER A:453 , HOH A:1085 , HOH A:1201 , LYS B:452BINDING SITE FOR RESIDUE SO4 A 1003
3AC3SOFTWAREARG A:467 , ASP A:481 , SER A:545BINDING SITE FOR RESIDUE SO4 A 1005
4AC4SOFTWARELYS B:502 , SER B:504 , HOH B:1255BINDING SITE FOR RESIDUE SO4 B 1001
5AC5SOFTWAREARG B:467 , GLN B:538 , HIS B:541 , HOH B:1369 , HOH B:1386 , HOH B:1431BINDING SITE FOR RESIDUE SO4 B 1004
6AC6SOFTWAREARG B:447 , ARG B:536 , GLU B:579 , HOH B:1317 , HOH B:1382BINDING SITE FOR RESIDUE SO4 B 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DPO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:418 -Pro A:419
2Ile B:418 -Pro B:419

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DPO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DPO)

(-) Exons   (0, 0)

(no "Exon" information available for 3DPO)

(-) 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:213
 aligned with DNAK_ECOLI | P0A6Y8 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:213
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598   
           DNAK_ECOLI   389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEI 601
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dpoA01 A:389-523 Substrate Binding Domain Of DNAk; Chain A, domain 1                                                                  3dpoA02 A:524-601  [code=1.20.1270.10, no name defined]                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee...eeeeee.......eeeeeeeee.......eeeeeee....hhhhheeeeeeee............eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpo A 389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEI 601
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598   


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with DNAK_ECOLI | P0A6Y8 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:215
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598     
           DNAK_ECOLI   389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQ 603
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dpoB01 B:389-523 Substrate Binding Domain Of DNAk; Chain A, domain 1                                                                  3dpoB02 B:524-603  [code=1.20.1270.10, no name defined]                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee...eeeeee.......eeeeeeeee.......eeeeeee....hhhhheeeeeeee............eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dpo B 389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQ 603
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598     


Chain C from PDB  Type:PROTEIN  Length:9
 aligned with PYRRH_PYRAP | P37362 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:9
          PYRRH_PYRAP     3 KGSYLPRPT  11
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...ee.... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3dpo C   0 KLYaLPRPT   8
                               |     
                               3-ALC 


Chain D from PDB  Type:PROTEIN  Length:9
 aligned with PYRRH_PYRAP | P37362 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:9
          PYRRH_PYRAP     3 KGSYLPRPT  11
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..eee.... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3dpo D   0 KLYaLPRPT   8
                               |     
                               3-ALC
   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 3DPO)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DPO)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DNAK_ECOLI | P0A6Y8)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
    GO:0044183    protein binding involved in protein folding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding.
    GO:0016989    sigma factor antagonist activity    The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0034620    cellular response to unfolded protein    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
    GO:0070389    chaperone cofactor-dependent protein refolding    The process of assisting in the restoration of the biological activity of an unfolded or misfolded protein, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0051085    chaperone mediated protein folding requiring cofactor    The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0043241    protein complex disassembly    The disaggregation of a protein complex into its constituent components. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:1903506    regulation of nucleic acid-templated transcription    Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D   (PYRRH_PYRAP | P37362)
biological process
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ALC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:418 - Pro A:419   [ RasMol ]  
    Ile B:418 - Pro B:419   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dpo
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DNAK_ECOLI | P0A6Y8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PYRRH_PYRAP | P37362
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DNAK_ECOLI | P0A6Y8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PYRRH_PYRAP | P37362
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DNAK_ECOLI | P0A6Y8: 1bpr 1dg4 1dkg 1dkx 1dky 1dkz 1q5l 2bpr 2kho 3dpp 3dpq 3qnj 4b9q 4e81 4ezn 4ezo 4ezp 4ezq 4ezr 4ezs 4ezt 4ezu 4ezv 4ezw 4ezx 4ezy 4ezz 4f00 4f01 4hy9 4hyb 4jn4 4jne 4jnf 4jwc 4jwd 4jwe 4jwi 4r5g 4r5i 4r5j 4r5k 4r5l
        PYRRH_PYRAP | P37362: 3dpp 3dpq 4ezn 4ezq 4hy9 4hyb 4j2o 5fdv 5hd1

(-) Related Entries Specified in the PDB File

3dpo 3dpq