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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF E.COLI DNAK IN COMPLEX WITH PR-BOMBESIN IN SPACE GROUP P21212
 
Authors :  M. Zahn, N. Straeter
Date :  03 May 12  (Deposition) - 24 Apr 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Biol. Unit 2:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Biol. Unit 4:  A,C  (1x)
Biol. Unit 5:  B,D  (1x)
Keywords :  Chaperone, Peptide Binding, Chaperone-Peptide Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zahn, N. Straeter
Structural Studies Of Dnak In Complex With Proline Rich Antimicrobial Peptides Reveal Two Different Peptide Binding Modes
To Be Published
PubMed: search

(-) 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: B0014, DNAK, GROP, GRPF, JW0013, SEG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: HSP70, HEAT SHOCK 70 KDA PROTEIN, HEAT SHOCK PROTEIN 70
 
Molecule 2 - PROLINE RICH BOMBESIN-RELATED PROTEIN
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 46-60
    Organism Common: CHINESE RED BELLY TOAD
    Organism Scientific: BOMBINA MAXIMA
    Organism Taxid: 161274
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN BOMBINA MAXIMA. C- TERMINUS IS AMIDATED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD
Biological Unit 2 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 3 (1x): ABCD
Biological Unit 4 (1x): A C 
Biological Unit 5 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4EZV)

(-) Sites  (0, 0)

(no "Site" information available for 4EZV)

(-) SS Bonds  (0, 0)

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

(-) 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 4EZV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EZV)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee...eeeeee.......eeeeeeeee......eeeeeeee....hhhhheeeeeeeee...........eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ezv A 389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHA 607
                                   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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee...eeeeee.......eeeeeeeee.......eeeeeee....hhhhheeeeeeee............eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ezv B 389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQ 604
                                   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:13
                                             
               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
                 4ezv C   5 PRPPQWAVGHFMM  17
                                    14   


Chain D from PDB  Type:PROTEIN  Length: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
                 4ezv D   7 PPQWAVGHFMM  17
                                    16
   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 4EZV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

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  Cis Peptide Bonds
    Ile A:418 - Pro A:419   [ RasMol ]  
    Ile B:418 - Pro B:419   [ RasMol ]  
 
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  Q8QFP2_BOMMX | Q8QFP2
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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 4ezw 4ezx 4ezy 4ezz 4f00 4f01 4hy9 4hyb 4jn4 4jne 4jnf 4jwc 4jwd 4jwe 4jwi 4r5g 4r5i 4r5j 4r5k 4r5l
UniProtKB/TrEMBL
        Q8QFP2_BOMMX | Q8QFP2: 4ezu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4EZV)