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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF E.COLI DNAK IN COMPLEX WITH PYRRHOCORICIN_LYZZ (RESIDUES 1 TO 11)
 
Authors :  M. Zahn, N. Straeter
Date :  13 Nov 12  (Deposition) - 17 Apr 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Chaperone, Antimicrobial Peptides, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zahn, N. Berthold, B. Kieslich, D. Knappe, R. Hoffmann, N. Strater
Structural Studies On The Forward And Reverse Binding Modes Of Peptides To The Chaperone Dnak.
J. Mol. Biol. V. 425 2463 2013
PubMed-ID: 23562829  |  Reference-DOI: 10.1016/J.JMB.2013.03.041

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN DNAK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 389-607
    Gene: DNAK, GROP, GRPF, SEG, B0014, JW0013
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: HSP70, HEAT SHOCK 70 KDA PROTEIN, HEAT SHOCK PROTEIN 70
 
Molecule 2 - PYRRHOCORICIN
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 1-11
    Organism Scientific: PYRRHOCORIS APTERUS
    Organism Taxid: 37000
    Other Details: PYRRHOCORICIN OCCURS NATURALLY IN PYRRHOCORIS APTERUS.
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ALC4Mod. Amino Acid2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ALC2Mod. Amino Acid2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ALC2Mod. Amino Acid2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:458 , ASP A:460 , HOH A:838 , HOH A:967BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWAREARG B:447 , ARG B:536 , GLU B:579 , HOH B:939BINDING SITE FOR RESIDUE SO4 B 701
3AC3SOFTWARELYS B:502 , SER B:504 , HOH B:814 , HOH B:890BINDING SITE FOR RESIDUE SO4 B 702
4AC4SOFTWAREMET A:404 , GLY A:405 , PRO C:8 , ARG C:9 , HOH C:203 , HOH C:207 , HOH C:208BINDING SITE FOR RESIDUE SO4 C 101
5AC5SOFTWAREILE A:401 , GLU A:402 , THR A:403 , MET A:404 , GLN A:424 , VAL A:425 , PHE A:426 , SER A:427 , THR A:428 , GLU A:430 , GLN A:433 , VAL A:436 , ARG A:467 , ILE A:472 , ASP A:540 , HOH A:942 , ASP B:510 , THR C:12 , SO4 C:101 , HOH C:201 , HOH C:202 , HOH C:203 , HOH C:204 , HOH C:206 , HOH C:209 , HOH C:211 , HOH C:213 , HOH C:214BINDING SITE FOR CHAIN C OF PYRRHOCORICIN
6AC6SOFTWAREARG A:517 , ASP A:518 , ILE B:401 , GLU B:402 , THR B:403 , MET B:404 , VAL B:425 , PHE B:426 , SER B:427 , THR B:428 , ALA B:429 , GLN B:433 , ALA B:435 , VAL B:436 , THR B:437 , ILE B:438 , GLY B:468 , HOH B:807 , HOH B:912 , THR D:12 , HOH D:101 , HOH D:103BINDING SITE FOR CHAIN D OF PYRRHOCORICIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HY9)

(-) 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 4HY9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HY9)

(-) Exons   (0, 0)

(no "Exon" information available for 4HY9)

(-) 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
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee...eeeeee.......eeeeeee.........eeeeeee....hhhhheeeeeeee............eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hy9 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
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee...eeeeee.......eeeeeeeee......eeeeeeee....hhhhheeeeeeeee...........eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hy9 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
                                         
               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
                 4hy9 C   4 LYaaPRPTT  12
                              ||     
                              6-ALC  
                               7-ALC 


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               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
                 4hy9 D   4 LYaaPRPTT  12
                              ||     
                              6-ALC  
                               7-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 4HY9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HY9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HY9)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

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  PYRRH_PYRAP | P37362
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 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 3dpo 3dpp 3dpq 3qnj 4b9q 4e81 4ezn 4ezo 4ezp 4ezq 4ezr 4ezs 4ezt 4ezu 4ezv 4ezw 4ezx 4ezy 4ezz 4f00 4f01 4hyb 4jn4 4jne 4jnf 4jwc 4jwd 4jwe 4jwi 4r5g 4r5i 4r5j 4r5k 4r5l
        PYRRH_PYRAP | P37362: 3dpo 3dpp 3dpq 4ezn 4ezq 4hyb 4j2o 5fdv 5hd1

(-) Related Entries Specified in the PDB File

1dkx 1dky 1dkz 3dpo 3dpp 3dpq 3qnj 4e81 4hyb