1WOB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A LOOP6 HINGE MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE, W168F, COMPLEXED TO SULFATE

Authors :   K. Eaazhisai, H. Balaram, P. Balaram, M. R. N. Murthy

Date :   12 Aug 04 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Triosephosphate Isomerase, Loop6, Sulfate, W168F (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Eaazhisai, H. Balaram, P. Balaram, M. R. N. Murthy
Structures Of Unliganded And Inhibitor Complexes Of W168F, A Loop6 Hinge Mutant Of Plasmodium Falciparum Triosephosphate Isomerase: Observation Of An Intermediate Position Of Loop6
J. Mol. Biol. V. 343 671 2004
PubMed-ID: 15465054 | Reference-DOI: 10.1016/J.JMB.2004.08.060
(for further references see the PDB file header)

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.3.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	AA200
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	MALARIA PARASITE P. FALCIPARUM
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833
	Synonym	:	TIM

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	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, 2)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:211 , GLY A:232 , ASN A:233 , HOH A:429 , HOH A:430	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	SER B:211 , GLY B:232 , ASN B:233 , HOH B:524 , HOH B:525	BINDING SITE FOR RESIDUE SO4 B 501
3	AC3	SOFTWARE	SER C:211 , GLY C:232 , ASN C:233 , HOH C:622	BINDING SITE FOR RESIDUE SO4 C 601
4	AC4	SOFTWARE	HOH C:621 , SER D:211 , GLY D:232 , ASN D:233 , HOH D:735 , HOH D:739	BINDING SITE FOR RESIDUE SO4 D 701

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_PLAFA	4-246	4	A:4-246 B:4-246 C:4-246 D:4-246
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_PLAFA	163-173	4	A:164-173 B:164-173 C:164-173 D:164-173

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_PLAFA	4-246	2	A:4-246 B:4-246 - -
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_PLAFA	163-173	2	A:164-173 B:164-173 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TIM_2	PS51440	Triosephosphate isomerase (TIM) family profile.	TPIS_PLAFA	4-246	2	- - C:4-246 D:4-246
2	TIM_1	PS00171	Triosephosphate isomerase active site.	TPIS_PLAFA	163-173	2	- - C:164-173 D:164-173

(no "Exon" information available for 1WOB)

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:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1woba_ A: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wobA00 A:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhh....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: A:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wob A   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLFAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1wobb_ B: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wobB00 B:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhhh....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: B:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wob B   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLFAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain C from PDB  Type:PROTEIN  Length:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1wobc_ C: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wobC00 C:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhh....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: C:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wob C   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLFAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain D from PDB  Type:PROTEIN  Length:246
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d1wobd_ D: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wobD00 D:3-248 Aldolase class I                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) --TIM-1wobD01 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) --TIM-1wobD02 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (2)
           Pfam domains (3) --TIM-1wobD03 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (3)
           Pfam domains (4) --TIM-1wobD04 D:5-244                                                                                                                                                                                                                             ---- Pfam domains (4)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhhh....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: D:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wob D   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLFAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Triosephosphate isomerase (TIM) (148)

Family: Triosephosphate isomerase (TIM) (128)

Protein domain: Triosephosphate isomerase (126)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (20)

1a	d1woba_	A:
1b	d1wobb_	B:
1c	d1wobc_	C:
1d	d1wobd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Malaria parasite p (Plasmodium falciparum) (13)

1a	1wobA00	A:3-248
1b	1wobB00	B:3-248
1c	1wobC00	C:3-248
1d	1wobD00	D:3-248

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: TIM (80)

Plasmodium falciparum (17)

1a	TIM-1wobD01	D:5-244
1b	TIM-1wobD02	D:5-244
1c	TIM-1wobD03	D:5-244
1d	TIM-1wobD04	D:5-244

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TPIS_PLAFA | Q07412)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0004807	triose-phosphate isomerase activity	Catalysis of the reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate.
biological process
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

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	1wob
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1vga	THE SAME PROTEIN OF UNLIGANDED FORM
1woa	THE SAME PROTEIN COMPLEXED WITH GLYCEROL-2-PHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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