1KHY - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF CLPB N TERMINAL DOMAIN, IMPLICATION TO THE PEPTIDE BINDING FUNCTION OF CLPB

Authors :   L. Jingzhi, S. Bingdong

Date :   01 Dec 01 (Deposition) - 04 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Alpha Helix, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Jingzhi, S. Bingdong
The Crystal Structure Of E. Coli Hsp100 Clpb N Terminal Domain, Implication To Peptide Binding Function Of Clpb
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CLPB PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN (RESIDUES 1-148)
	Gene	:	CLPB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	HEAT SHOCK PROTEIN F84.1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1KHY)

(no "SS Bond" information available for 1KHY)

(no "Cis Peptide Bond" information available for 1KHY)

(no "SAP(SNP)/Variant" information available for 1KHY)

(no "PROSITE Motif" information available for 1KHY)

(no "Exon" information available for 1KHY)

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:132
 aligned with CLPB_ECOLI | P63284 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:139
                                    13        23        33        43        53        63        73        83        93       103       113       123       133         
           CLPB_ECOLI     4 DRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQ 142
               SCOP domains d1khya_ A: N-terminal domain of ClpB (heat shock protein F84.1)                                                                             SCOP domains
               CATH domains 1khyA00 A:4-142 Double Clp-N motif                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhh.....-------..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khy A   4 DRLTNKFQLALADAQSLALGHDNQFIEPLHLmSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQV-------QPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQ 142
                                    13        23        33 |      43        53        63        73|       83        93       103       113       123       133         
                                                          35-MSE                                 74      82

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with CLPB_ECOLI | P63284 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
           CLPB_ECOLI     3 LDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQ 142
               SCOP domains d1khyb_ B: N-terminal domain of ClpB (heat shock protein F84.1)                                                                              SCOP domains
               CATH domains 1khyB00 B:3-142 Double Clp-N motif                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhh...-------..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khy B   3 LDRLTNKFQLALADAQSLALGHDNQFIEPLHLmSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQV-------QPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQ 142
                                    12        22        32  |     42        52        62        72 |      82        92       102       112       122       132       142
                                                           35-MSE                                 74      82

Chain C from PDB  Type:PROTEIN  Length:135
 aligned with CLPB_ECOLI | P63284 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           CLPB_ECOLI     4 DRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQM 143
               SCOP domains d1khyc_ C: N-terminal domain of ClpB (heat shock protein F84.1)                                                                              SCOP domains
               CATH domains 1khyC00 C:4-142 Double Clp-N motif                                                                                                         - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....eehhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhh...-----..eehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khy C   4 DRLTNKFQLALADAQSLALGHDNQFIEPLHLmSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQV-----DVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQm 143
                                    13        23        33 |      43        53        63        73|     | 83        93       103       113       123       133       143
                                                          35-MSE                                 74    80                                                            143-MSE

Chain D from PDB  Type:PROTEIN  Length:140
 aligned with CLPB_ECOLI | P63284 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           CLPB_ECOLI     4 DRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQM 143
               SCOP domains d1khyd_ D: N-terminal domain of ClpB (heat shock protein F84.1)                                                                              SCOP domains
               CATH domains 1khyD00 D:4-142 Double Clp-N motif                                                                                                         - CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------Clp_N-1khyD01 D:94-143                             Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------Clp_N-1khyD02 D:94-143                             Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------Clp_N-1khyD03 D:94-143                             Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------Clp_N-1khyD04 D:94-143                             Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------Clp_N-1khyD05 D:94-143                             Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------Clp_N-1khyD06 D:94-143                             Pfam domains (6)
           Pfam domains (7) ------------------------------------------------------------------------------------------Clp_N-1khyD07 D:94-143                             Pfam domains (7)
           Pfam domains (8) ------------------------------------------------------------------------------------------Clp_N-1khyD08 D:94-143                             Pfam domains (8)
         Sec.struct. author .eehhhhhhhhhhhhhhhhh....eehhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhh............eehhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1khy D   4 DRLTNKFQLALADAQSLALGHDNQFIEPLHLmSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQm 143
                                    13        23        33 |      43        53        63        73        83        93       103       113       123       133       143
                                                          35-MSE                                                                                                     143-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Double Clp-N motif (13)

Superfamily: Double Clp-N motif (13)

Family: Double Clp-N motif (13)

Protein domain: N-terminal domain of ClpB (heat shock protein F84.1) (2)

Escherichia coli [TaxId: 562] (1)

1a	d1khya_	A:
1b	d1khyb_	B:
1c	d1khyc_	C:
1d	d1khyd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Double Clp-N motif (16)

Homologous Superfamily: Double Clp-N motif (16)

Escherichia coli. Organism_taxid: 562. (3)

1a	1khyD00	D:4-142
1b	1khyC00	C:4-142
1c	1khyB00	B:3-142
1d	1khyA00	A:4-142

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Clp_N] (16)

Family: Clp_N (16)

Escherichia coli (strain K12) (11)

1a	Clp_N-1khyD01	D:94-143
1b	Clp_N-1khyD02	D:94-143
1c	Clp_N-1khyD03	D:94-143
1d	Clp_N-1khyD04	D:94-143
1e	Clp_N-1khyD05	D:94-143
1f	Clp_N-1khyD06	D:94-143
1g	Clp_N-1khyD07	D:94-143
1h	Clp_N-1khyD08	D:94-143

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CLPB_ECOLI | P63284)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0042623	ATPase activity, coupled	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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).
biological process
	GO:0019538	protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	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.
	GO:0006986	response to unfolded protein	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 an unfolded protein stimulus.
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.

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	1khy
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	CLPB_ECOLI \| P63284	:	1jbk 4ciu 4d2q 4d2u 4d2x

1jbk	CRYSTAL STRUCTURE OF THE FIRST NUCELOTIDE BINDING DOMAIN OF CLPB

Description

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Ligands, Modified Residues, Ions (1, 6)

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