3OPD - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF AN HSP90 FROM TRYPANOSOMA BRUCEI, TB10.26.1080 IN THE PRESENCE OF A BENZAMIDE DERIVATIVE

Authors :   J. C. Pizarro, A. K. Wernimont, A. Hutchinson, H. Sullivan, K. Chamberl J. Weadge, D. Cossar, Y. Li, I. Kozieradzki, A. Bochkarev, C. H. Arrows A. M. Edwards, C. Bountra, J. Weigelt, P. G. Wyatt, A. H. Fairlamb, C. Ma M. A. J. Ferguson, R. Hui, T. Hills, Structural Genomics Consortium

Date :   31 Aug 10 (Deposition) - 13 Oct 10 (Release) - 13 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Chaperone, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Pizarro, A. K. Wernimont, A. Hutchinson, H. Sullivan, K. Chamberlain, J. Weadge, D. Cossar, Y. Li, I. Kozieradzki, A. Bochkarev, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, P. G. Wyatt, A. H. Fairlamb, C. Mackenzie, M. A. J. Ferguson, R. Hui, T. Hills, Structural Genomics Consortium (Sgc)
Crystal Structure Of The N-Terminal Domain Of An Hsp90 From Trypanosoma Brucei, Tb10. 26. 1080 In The Presence Of A Benzamide Derivative
To Be Published
PubMed: search

Molecule 1 - HEAT SHOCK PROTEIN 83
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	HSP83, TB10.26.1080
	Organism Scientific	:	TRYPANOSOMA BRUCEI BRUCEI
	Organism Taxid	:	5702

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	HIE	3	Ligand/Ion	4-[6,6-DIMETHYL-4-OXO-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-INDAZOL-1-YL]-2-[(CIS-4-HYDROXYCYCLOHEXYL)AMINO]BENZAMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	HIE	1	Ligand/Ion	4-[6,6-DIMETHYL-4-OXO-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-INDAZOL-1-YL]-2-[(CIS-4-HYDROXYCYCLOHEXYL)AMINO]BENZAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HIE	1	Ligand/Ion	4-[6,6-DIMETHYL-4-OXO-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-INDAZOL-1-YL]-2-[(CIS-4-HYDROXYCYCLOHEXYL)AMINO]BENZAMIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	HIE	1	Ligand/Ion	4-[6,6-DIMETHYL-4-OXO-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-INDAZOL-1-YL]-2-[(CIS-4-HYDROXYCYCLOHEXYL)AMINO]BENZAMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:36 , ALA A:40 , LYS A:43 , ASP A:78 , MET A:83 , ASN A:91 , LEU A:92 , ILE A:95 , ALA A:96 , GLY A:120 , TYR A:124 , TRP A:147 , THR A:169 , ILE A:171 , HOH A:239 , HOH A:248 , HOH A:355 , HOH A:356	BINDING SITE FOR RESIDUE HIE A 214
2	AC2	SOFTWARE	ASN B:36 , ALA B:40 , ASP B:78 , MET B:83 , ASN B:91 , LEU B:92 , ALA B:96 , GLY B:120 , PHE B:123 , TYR B:124 , TRP B:147 , THR B:169 , ILE B:171 , HOH B:221 , HOH B:283	BINDING SITE FOR RESIDUE HIE B 214
3	AC3	SOFTWARE	ASN C:36 , ALA C:40 , ASP C:78 , MET C:83 , ASN C:91 , LEU C:92 , ALA C:96 , GLY C:120 , VAL C:121 , PHE C:123 , TYR C:124 , TRP C:147 , ILE C:171	BINDING SITE FOR RESIDUE HIE C 214

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

Asymmetric Unit

No.	Residues
1	Pro A:161	-	Asp A:162
2	Ser C:53	-	Val C:54

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HSP90	PS00298	Heat shock hsp90 proteins family signature.	HSP83_TRYBB	23-32	3	A:23-32 B:23-32 C:23-32

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HSP90	PS00298	Heat shock hsp90 proteins family signature.	HSP83_TRYBB	23-32	1	A:23-32 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HSP90	PS00298	Heat shock hsp90 proteins family signature.	HSP83_TRYBB	23-32	1	- B:23-32 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HSP90	PS00298	Heat shock hsp90 proteins family signature.	HSP83_TRYBB	23-32	1	- - C:23-32

(no "Exon" information available for 3OPD)

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:208
 aligned with HSP83_TRYBB | P12861 from UniProtKB/Swiss-Prot  Length:703

    Alignment length:210
                             1                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
          HSP83_TRYBB     - -MTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNSSDACDKIRYQSLTNQSVLGDEPHLRIRVIPDRVNKTLTVEDSGIGMTKADLVNNLGTIARSGTKSFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVVSKNNEDDAYTWESSAGGTFTVTSTPDCDLKRGTRIVLHLKEDQQEYLEERRLKDLIKKHSEFIGYDIELMVEN 209
               SCOP domains d3opda_ A: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee.....hhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee...--...eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------HSP90     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3opd A   0 GMTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNSSDACDKIRYQSLTNQSVLGDEPHLRIRVIPDRVNKTLTVEDSGIGMTKADLVNNLGTIARSGTKSFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVVSKNNEDDAYTWESSAGGTFTVTSTPD--LKRGTRIVLHLKEDQQEYLEERRLKDLIKKHSEFIGYDIELMVEN 209
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  |  | 169       179       189       199       209
                                                                                                                                                                                            162  |                                            
                                                                                                                                                                                               165

Chain B from PDB  Type:PROTEIN  Length:205
 aligned with HSP83_TRYBB | P12861 from UniProtKB/Swiss-Prot  Length:703

    Alignment length:209
                             1                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199         
          HSP83_TRYBB     - -MTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNSSDACDKIRYQSLTNQSVLGDEPHLRIRVIPDRVNKTLTVEDSGIGMTKADLVNNLGTIARSGTKSFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVVSKNNEDDAYTWESSAGGTFTVTSTPDCDLKRGTRIVLHLKEDQQEYLEERRLKDLIKKHSEFIGYDIELMVE 208
               SCOP domains d3opdb_ B: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....eeeeee.....hhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee..----..eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------HSP90     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3opd B   0 GMTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNSSDACDKIRYQSLTNQSVLGDEPHLRIRVIPDRVNKTLTVEDSGIGMTKADLVNNLGTIARSGTKSFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVVSKNNEDDAYTWESSAGGTFTVTSTP----KRGTRIVLHLKEDQQEYLEERRLKDLIKKHSEFIGYDIELMVE 208
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 |    |169       179       189       199         
                                                                                                                                                                                           161  166

Chain C from PDB  Type:PROTEIN  Length:202
 aligned with HSP83_TRYBB | P12861 from UniProtKB/Swiss-Prot  Length:703

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
          HSP83_TRYBB     1 MTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNSSDACDKIRYQSLTNQSVLGDEPHLRIRVIPDRVNKTLTVEDSGIGMTKADLVNNLGTIARSGTKSFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVVSKNNEDDAYTWESSAGGTFTVTSTPDCDLKRGTRIVLHLKEDQQEYLEERRLKDLIKKHSEFIGYDIELMVEN 209
               SCOP domains d3opdc_ C: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------HATPase_c_3-3opdC01 C:23-185                                                                                                                                       -----------   ---------- Pfam domains (1)
           Pfam domains (2) ----------------------HATPase_c_3-3opdC02 C:23-185                                                                                                                                       -----------   ---------- Pfam domains (2)
           Pfam domains (3) ----------------------HATPase_c_3-3opdC03 C:23-185                                                                                                                                       -----------   ---------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------    --------------------------------------------------------------------------------------------------------------------------HSP90-3opdC04 C:   181-209    Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------    --------------------------------------------------------------------------------------------------------------------------HSP90-3opdC05 C:   181-209    Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------    --------------------------------------------------------------------------------------------------------------------------HSP90-3opdC06 C:   181-209    Pfam domains (6)
         Sec.struct. author .eeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...----....eeeeee....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee........eeeeeeee.hhhhhhhhhhhhhhhhhhh.---...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------HSP90     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3opd C   1 MTETFAFQAEINQLMSLIINTFYSNKEIFLRELISNSSDACDKIRYQSLTNQSV----PHLRIRVIPDRVNKTLTVEDSGIGMTKADLVNNLGTIARSGTKSFMEALEAGGDMSMIGQFGVGFYSAYLVADRVTVVSKNNEDDAYTWESSAGGTFTVTSTPDCDLKRGTRIVLHLKEDQQEYLEERRLKDLIKKHS---GYDIELMVEN 209
                                    10        20        30        40        50   |    60        70        80        90       100       110       120       130       140       150       160       170       180       190     | 200         
                                                                                54   59                                                                                                                                      196 200

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 "CATH Domain" information available for 3OPD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: His_Kinase_A (147)

Family: HATPase_c_3 (11)

Trypanosoma brucei brucei (1)

1a	HATPase_c_3-3opdC01	C:23-185
1b	HATPase_c_3-3opdC02	C:23-185
1c	HATPase_c_3-3opdC03	C:23-185

Clan: no clan defined [family: HSP90] (107)

Family: HSP90 (107)

Trypanosoma brucei brucei (1)

2a	HSP90-3opdC04	C:181-209
2b	HSP90-3opdC05	C:181-209
2c	HSP90-3opdC06	C:181-209

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (HSP83_TRYBB | P12861)

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: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:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	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:0042026	protein refolding	The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
	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:0006950	response to stress	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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	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:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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