3QNJ - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF E.COLI DNAK IN COMPLEX WITH THE ANTIMICROBIAL PEPTIDE ONCOCIN

Authors :   M. Zahn, N. Straeter

Date :   08 Feb 11 (Deposition) - 23 Mar 11 (Release) - 11 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x)

Keywords :   Peptide/Protein Binding, Chaperone-Antimicrobial Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Knappe, M. Zahn, U. Sauer, G. Schiffer, N. Strater, R. Hoffmann
Rational Design Of Oncocin Derivatives With Superior Protease Stabilities And Antibacterial Activities Based On The High-Resolution Structure Of The Oncocin-Dnak Complex.
Chembiochem V. 12 874 2011
PubMed-ID: 21387510 | Reference-DOI: 10.1002/CBIC.201000792

Molecule 1 - CHAPERONE PROTEIN DNAK
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 389-607
	Gene	:	DNAK, GROP, GRPF, SEG
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	HSP70, HEAT SHOCK 70 KDA PROTEIN, HEAT SHOCK PROTEIN 70

Molecule 2 - ANTIMICROBIAL PEPTIDE ONCOCIN
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	ONCOPELTUS FASCIATUS
	Organism Taxid	:	7536
	Other Details	:	THIS SEQUENCE IS DERIVED FROM ONCOPELTUS FASCIATUS AND OPTIMIZED FOR THE TREATMENT OF GRAM-NEGATIVE PATHOGENS
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:153 , HOH A:165 , LYS A:452 , SER A:453 , LYS B:452	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	HOH B:152 , LYS B:502 , SER B:504	BINDING SITE FOR RESIDUE SO4 B 2
3	AC3	SOFTWARE	ARG B:447 , ARG B:536 , LYS B:577 , GLU B:579	BINDING SITE FOR RESIDUE SO4 B 4
4	AC4	SOFTWARE	GLU B:402 , GLY B:405 , GLY B:406 , PRO D:8	BINDING SITE FOR RESIDUE SO4 B 5
5	AC5	SOFTWARE	ASP A:510 , HOH B:120 , ASN B:458	BINDING SITE FOR RESIDUE SO4 B 6
6	AC6	SOFTWARE	HOH A:119 , MET A:404 , GLY A:405 , ARG C:9	BINDING SITE FOR RESIDUE SO4 C 20

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 3QNJ)

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:204
 aligned with DNAK_ECOLI | P0A6Y8 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:210
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598
           DNAK_ECOLI   389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKL 598
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee...eeeeee.......eeeeeee.........eeeeeee....hhhhheeeeeeee............eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qnj A 389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQV------LPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKL 598
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548 |     558       568       578       588       598
                                                                                                                                                                                           550    557

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with DNAK_ECOLI | P0A6Y8 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:214
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598    
           DNAK_ECOLI   389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIA 602
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) HSP70-3qnjB01 B:389-602                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) HSP70-3qnjB02 B:389-602                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author .....ee...eeeee...eeeeee...ee..eeeeeeeee......eeeeeeee....hhhhheeeeeeeee...........eeeeeee.....eeeeeee.....eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnj B 389 VLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEE---KLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIA 602
                                   398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548   |   558       568       578       588       598    
                                                                                                                                                                                             552 556

Chain C from PDB  Type:PROTEIN  Length:8
                                        
               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
                 3qnj C   3 KPPYLPRP  10

Chain D from PDB  Type:PROTEIN  Length:10
                                          
               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
                 3qnj D   4 PPYLPRPRPP  13
                                    13

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 '\|'

(no "SCOP Domain" information available for 3QNJ)

(no "CATH Domain" information available for 3QNJ)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: HSP70 (41)

Escherichia coli (strain K12) (4)

1a	HSP70-3qnjB01	B:389-602
1b	HSP70-3qnjB02	B:389-602

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.

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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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	3qnj
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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