3WT1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE B'-A' DOMAIN OF THERMOPHILIC FUNGAL PROTEIN DISULFIDE ISOMERASE (REDUCED FORM)

Authors :   K. Inagaki, T. Satoh, S. G. Itoh, H. Okumura, K. Kato

Date :   02 Apr 14 (Deposition) - 26 Nov 14 (Release) - 31 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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 :   Thioredoxin Fold, Isomerase, Disulfide Bond, Endoplasmic Reticulum, Redox-Active Center, Thioredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Inagaki, T. Satoh, S. G. Itoh, H. Okumura, K. Kato
Redox-Dependent Conformational Transition Of Catalytic Domain Of Protein Disulfide Isomerase Indicated By Crystal Structure-Based Molecular Dynamics Simulation
Chem. Phys. Lett. V. 618 203 2015
PubMed: search | Reference-DOI: 10.1016/J.CPLETT.2014.11.017

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.3.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 278-469
	Organism Common	:	SOFT-ROT FUNGUS
	Organism Scientific	:	HUMICOLA INSOLENS
	Organism Taxid	:	34413
	Synonym	:	PDI

		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, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:218 , HIS A:270 , SER C:385 , GLU C:386	BINDING SITE FOR RESIDUE GOL A 501
2	AC2	SOFTWARE	TYR B:218 , SER D:385 , GLU D:386 , ALA D:449	BINDING SITE FOR RESIDUE GOL B 501
3	AC3	SOFTWARE	GLU A:386 , TYR C:218	BINDING SITE FOR RESIDUE GOL C 501
4	AC4	SOFTWARE	SER B:385 , TYR D:218	BINDING SITE FOR RESIDUE GOL D 501

(no "SS Bond" information available for 3WT1)

Asymmetric Unit

No.	Residues
1	Phe A:281	-	Pro A:282
2	Phe A:410	-	Pro A:411
3	Phe B:281	-	Pro B:282
4	Phe B:410	-	Pro B:411
5	Phe C:281	-	Pro C:282
6	Phe C:410	-	Pro C:411
7	Phe D:281	-	Pro D:282
8	Phe D:410	-	Pro D:411

(no "SAP(SNP)/Variant" information available for 3WT1)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	PDI_HUMIN	7-128 335-465	4	- A:315-445 B:315-445 C:315-445 D:315-445
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDI_HUMIN	42-60 377-395	4	- A:357-375 B:357-375 C:357-375 D:357-375

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	PDI_HUMIN	7-128 335-465	1	- A:315-445 - - -
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDI_HUMIN	42-60 377-395	1	- A:357-375 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	PDI_HUMIN	7-128 335-465	1	- - B:315-445 - -
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDI_HUMIN	42-60 377-395	1	- - B:357-375 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	PDI_HUMIN	7-128 335-465	1	- - - C:315-445 -
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDI_HUMIN	42-60 377-395	1	- - - C:357-375 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	PDI_HUMIN	7-128 335-465	1	- - - - D:315-445
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDI_HUMIN	42-60 377-395	1	- - - - D:357-375

(no "Exon" information available for 3WT1)

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:244
 aligned with PDI_HUMIN | P55059 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:244
                                   235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465    
            PDI_HUMIN   226 ATPLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 469
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.......eeeeee....eeee.......hhhhhhhhhhhhhh....................eeehhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..............eeeee........ee.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------THIOREDOXIN_2  PDB: A:315-445 UniProt: 335-465                                                                                     ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_1      -------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wt1 A 206 GSPLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 449
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with PDI_HUMIN | P55059 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:242
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
            PDI_HUMIN   228 PLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 469
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.......eeeeee....eeee.......hhhhhhhhhhhhhh....................eeehhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..............eeeee........ee.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------THIOREDOXIN_2  PDB: B:315-445 UniProt: 335-465                                                                                     ---- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_1      -------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wt1 B 208 PLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 449
                                   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447

Chain C from PDB  Type:PROTEIN  Length:242
 aligned with PDI_HUMIN | P55059 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:242
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
            PDI_HUMIN   228 PLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 469
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.......eeeeee....eeee.......hhhhhhhhhhhhhh....................eeehhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..............eeeee........ee.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------THIOREDOXIN_2  PDB: C:315-445 UniProt: 335-465                                                                                     ---- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_1      -------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wt1 C 208 PLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 449
                                   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447

Chain D from PDB  Type:PROTEIN  Length:242
 aligned with PDI_HUMIN | P55059 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:242
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
            PDI_HUMIN   228 PLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 469
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.......eeeeee....eeee.......hhhhhhhhhhhhhh....................eeehhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhhhh.....eeeeeee..............eeeee........ee.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------THIOREDOXIN_2  PDB: D:315-445 UniProt: 335-465                                                                                     ---- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_1      -------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wt1 D 208 PLIGEIGPETYSDYMSAGIPLAYIFAETAEERKELSDKLKPIAEAQRGVINFGTIDAKAFGAHAGNLNLKTDKFPAFAIQEVAKNQKFPFDQEKEITFEAIKAFVDDFVAGKIEPSIKSEPIPEKQEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA 449
                                   217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447

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 3WT1)

(no "CATH Domain" information available for 3WT1)

(no "Pfam Domain" information available for 3WT1)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PDI_HUMIN | P55059)

molecular function
	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:0003756	protein disulfide isomerase activity	Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:281 - Pro A:282	[ RasMol ]
		Phe A:410 - Pro A:411	[ RasMol ]
		Phe B:281 - Pro B:282	[ RasMol ]
		Phe B:410 - Pro B:411	[ RasMol ]
		Phe C:281 - Pro C:282	[ RasMol ]
		Phe C:410 - Pro C:411	[ RasMol ]
		Phe D:281 - Pro D:282	[ RasMol ]
		Phe D:410 - Pro D:411	[ RasMol ]

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	3wt1
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	5.3.4.1
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	PDI_HUMIN \| P55059	:	2djj 2djk 2kp1 2kp2 2rue 2ruf 3wt2 5crw

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SS Bonds (0, 0)

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