2B5E - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YEAST PROTEIN DISULFIDE ISOMERASE

Authors :   H. Schindelin, G. Tian

Date :   28 Sep 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Protein Disulfide Isomerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Tian, S. Xiang, R. Noiva, W. J. Lennarz, H. Schindelin
The Crystal Structure Of Yeast Protein Disulfide Isomerase Suggests Cooperativity Between Its Active Sites.
Cell(Cambridge, Mass. ) V. 124 61 2006
PubMed-ID: 16413482 | Reference-DOI: 10.1016/J.CELL.2005.10.044

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE
	Chains	:	A
	EC Number	:	5.3.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PTYB12
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	PDI1, MFP1, TRG1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PDI, THIOREDOXIN-RELATED GLYCOPROTEIN 1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	BA	1	Ligand/Ion	BARIUM ION
2	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:123 , GLU A:194 , HOH A:555 , HOH A:599	BINDING SITE FOR RESIDUE BA A 1
2	AC2	SOFTWARE	GLU A:272 , LEU A:344 , GLU A:345 , SER A:346	BINDING SITE FOR RESIDUE GOL A 523
3	AC3	SOFTWARE	GLU A:99 , HIS A:100 , SER A:119	BINDING SITE FOR RESIDUE GOL A 524

Asymmetric/Biological Unit

No.	Residues
1	A:61	-	A:64
2	A:90	-	A:97

Asymmetric/Biological Unit

No.	Residues
1	Phe A:105	-	Pro A:106
2	Phe A:311	-	Pro A:312
3	Tyr A:450	-	Pro A:451

(no "SAP(SNP)/Variant" information available for 2B5E)

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	PDI_YEAST	15-141 356-485	1	- A:356-485
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDI_YEAST	53-71 398-416	2	A:53-71 A:398-416

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YCL043C	1	YCL043C.1	III:50221-48653	1569	PDI_YEAST	1-522	522	1	A:22-504	483

Asymmetric/Biological 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:483
 aligned with PDI_YEAST | P17967 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:483
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   
            PDI_YEAST    22 AQQEAVAPEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEKNITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSAENADDDFKLSIYLPSAMDEPVVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFYNDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRHAGNLNMKEQFPLFAIHDMTEDLKYGLPQLSEEAFDELSDKIVLESKAIESLVKDFLKGDASPIVKSQEIFENQDSSVFQLVGKNHDEIVNDPKKDVLVLYYAPWCGHCKRLAPTYQELADTYANATSDVLIAKLDHTENDVRGVVIEGYPTIVLYPGGKKSESVVYQGSRSLDSLFDFIKENGHFDVDGKALYEEAQEKAAEE 504
               SCOP domains -d2b5ea4 A:23-141 Protein disulfide isomerase, PDI                                                                      d2b5ea2 A:142-239 Protein disulfide isomerase, PDI                                                d2b5ea3 A:240-364 Protein disulfide isomerase, PDI                                                                           d2b5ea1 A:365-504 Protein disulfide isomerase, PDI                                                                                           SCOP domains
               CATH domains 2b5eA01 A:22-140 Glutaredoxin                                                                                          --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2b5eA04 A:365-504 Glutaredoxin                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee....hhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhh......eeeeee......eee.....hhhhhhhhhhhhh...eee..hhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh....eeeeee......eeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......eeeeee....eeee....hhhhhhh.......hhhhhhhhhhhhhhh..................eeee...hhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhh...........eeeee...............hhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: - UniProt: 15-141                                                                                   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_2  PDB: A:356-485 UniProt: 356-485                                                                                    ------------------- PROSITE (1)
                PROSITE (2) -------------------------------THIOREDOXIN_1      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:22-504 UniProt: 1-522 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                 Transcript 1
                 2b5e A  22 MQQEAVAPEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEKNITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSAENADDDFKLSIYLPSAMDEPVVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFYNDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRHAGNLNMKEQFPLFAIHDMTEDLKYGLPQLSEEAFDELSDKIVLESKAIESLVKDFLKGDASPIVKSQEIFENQDSSVFQLVGKNHDEIVNDPKKDVLVLYYAPWCGHCKRLAPTYQELADTYANATSDVLIAKLDHTENDVRGVVIEGYPTIVLYPGGKKSESVVYQGSRSLDSLFDFIKENGHFDVDGKALYEEAQEKAAEE 504
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: PDI-like (13)

Protein domain: Protein disulfide isomerase, PDI (9)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d2b5ea1	A:365-504
1b	d2b5ea2	A:142-239
1c	d2b5ea3	A:240-364
1d	d2b5ea4	A:23-141

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Baker's yeast (Saccharomyces cerevisiae) (19)

1a	2b5eA01	A:22-140
1b	2b5eA04	A:365-504

(no "Pfam Domain" information available for 2B5E)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PDI_YEAST | P17967)

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: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:0003756	protein disulfide isomerase activity	Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	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:0034976	response to endoplasmic reticulum stress	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 a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:105 - Pro A:106	[ RasMol ]
		Phe A:311 - Pro A:312	[ RasMol ]
		Tyr A:450 - Pro A:451	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2b5e
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PDI_YEAST \| P17967
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	5.3.4.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PDI_YEAST \| P17967
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PDI_YEAST \| P17967	:	3boa

1a8y	CRYSTAL STRUCTURE OF CALSEQUESTRIN
1eej	CRYSTAL STRUCTURE OF E.COLI PROTEIN DISULFIDE ISOMERASE DSBC
1mek	NMR STRUCTURE OF HUMAN PDI DOMAIN A
1v57	CRYSTAL STRUCTURE OF E.COLI PROTEIN DISULFIDE ISOMERASE DSBG
2bjx	NMR STRUCTURE OF HUMAN PDI DOMAIN B
2trx	CRYSTAL STRUCTURE OF E.COLI THIOREDOXIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File