3UVT - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE THIRD CATALYTIC DOMAIN OF ERP46

Authors :   G. Kozlov, I. E. Gulerez, K. Gehring

Date :   30 Nov 11 (Deposition) - 11 Apr 12 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)

Keywords :   Thioredoxin-Like Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. E. Gulerez, G. Kozlov, A. Rosenauer, K. Gehring
Structure Of The Third Catalytic Domain Of The Protein Disulfide Isomerase Erp46.
Acta Crystallogr. , Sect. F V. 68 378 2012
PubMed-ID: 22505402 | Reference-DOI: 10.1107/S1744309112005866

Molecule 1 - THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5
	Chains	:	A, B, C, D, E
	EC Number	:	5.3.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN 3
	Gene	:	TXNDC5, TLP46, UNQ364/PRO700
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ENDOPLASMIC RETICULUM RESIDENT PROTEIN 46, ER PROTEIN 46, ERP46, THIOREDOXIN-LIKE PROTEIN P46

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 2)

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

Biological Unit 5 (0, 0)

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

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:413 , GLY A:414 , ARG A:415	BINDING SITE FOR RESIDUE SO4 A 5
2	AC2	SOFTWARE	HOH B:67 , LYS B:406 , LYS B:407 , HOH B:457	BINDING SITE FOR RESIDUE SO4 B 3
3	AC3	SOFTWARE	HOH C:260 , ARG C:422 , HOH C:441	BINDING SITE FOR RESIDUE SO4 C 2
4	AC4	SOFTWARE	HOH C:124 , LYS C:366 , GLU C:367 , HOH C:444 , ARG D:422	BINDING SITE FOR RESIDUE SO4 D 1
5	AC5	SOFTWARE	PRO C:369 , ASP D:418 , ARG D:422	BINDING SITE FOR RESIDUE SO4 D 4

Asymmetric Unit

No.	Residues
1	A:381	-	A:388
2	B:350	-	B:353
3	B:381	-	B:388
4	C:381	-	C:388
5	D:381	-	D:388

Asymmetric Unit

No.	Residues
1	Tyr A:396	-	Pro A:397
2	Tyr B:396	-	Pro B:397
3	Tyr C:396	-	Pro C:397
4	Tyr D:396	-	Pro D:397
5	Tyr E:396	-	Pro E:397

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

Asymmetric Unit (1, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TXND5_HUMAN	81-99 209-227 342-360	5	- - A:342-360 B:342-360 C:342-360 D:342-360 E:342-360

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TXND5_HUMAN	81-99 209-227 342-360	1	- - A:342-360 - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TXND5_HUMAN	81-99 209-227 342-360	1	- - - B:342-360 - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TXND5_HUMAN	81-99 209-227 342-360	1	- - - - C:342-360 - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TXND5_HUMAN	81-99 209-227 342-360	1	- - - - - D:342-360 -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TXND5_HUMAN	81-99 209-227 342-360	1	- - - - - - E:342-360

Asymmetric Unit (4, 17)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000379757	1	ENSE00001482400	chr6:7911047-7910747	301	TXND5_HUMAN	1-88	88	0	-	-
1.3	ENST00000379757	3	ENSE00002035816	chr6:7904956-7904807	150	TXND5_HUMAN	88-138	51	0	-	-
1.4b	ENST00000379757	4b	ENSE00002030712	chr6:7899914-7899809	106	TXND5_HUMAN	138-173	36	0	-	-
1.5b	ENST00000379757	5b	ENSE00002020031	chr6:7895435-7895339	97	TXND5_HUMAN	174-206	33	0	-	-
1.6	ENST00000379757	6	ENSE00002062288	chr6:7891969-7891854	116	TXND5_HUMAN	206-244	39	0	-	-
1.7	ENST00000379757	7	ENSE00002051337	chr6:7889814-7889728	87	TXND5_HUMAN	245-273	29	0	-	-
1.8c	ENST00000379757	8c	ENSE00002072823	chr6:7889081-7888938	144	TXND5_HUMAN	274-321	48	2	- B:321-321 C:319-321 - -	- 1 3 - -
1.9	ENST00000379757	9	ENSE00002061487	chr6:7886276-7886194	83	TXND5_HUMAN	322-349	28	5	A:322-349 B:322-349 C:322-349 D:322-349 E:324-346	28 28 28 28 23
1.10	ENST00000379757	10	ENSE00002026226	chr6:7884721-7884592	130	TXND5_HUMAN	349-392	44	5	A:349-392 (gaps) B:349-392 (gaps) C:349-392 D:349-392 E:353-392 (gaps)	44 44 44 44 40
1.11c	ENST00000379757	11c	ENSE00001964269	chr6:7883499-7881750	1750	TXND5_HUMAN	393-432	40	5	A:393-428 B:393-428 C:393-428 D:393-428 E:393-428	36 36 36 36 36

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:106
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:107
                                   331       341       351       361       371       381       391       401       411       421       
          TXND5_HUMAN   322 GTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
               SCOP domains d3uvta_ A: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhhh..eeeeeee...hhhhhhhhhhhhhhhh.....-..eeeeeee...hhhhhhhh......eeeeee..eeeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------THIOREDOXIN_1      -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---------------------------Exon 1.10  PDB: A:349-392 (gaps)            Exon 1.11c  PDB: A:393-428           Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:322-349    ------------------------------------------------------------------------------- Transcript 1 (2)
                 3uvt A 322 STVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPG-AGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
                                   331       341       351       361        |-|      381       391       401       411       421       
                                                                          370 |                                                        
                                                                            372

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:108
                                   330       340       350       360       370       380       390       400       410       420        
          TXND5_HUMAN   321 KGTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
               SCOP domains d3uvtb_ B: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....hhhhhhh..eeeeeee...hhhhhhhhhhhhhhh......-..eeeeeee...hhhhhhhh......eeeeee..eeeee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1---------------------------Exon 1.10  PDB: B:349-392 (gaps)            Exon 1.11c  PDB: B:393-428           Transcript 1 (1)
           Transcript 1 (2) -Exon 1.9  PDB: B:322-349    ------------------------------------------------------------------------------- Transcript 1 (2)
                 3uvt B 321 GSTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPG-AGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
                                   330       340       350       360       370 |     380       390       400       410       420        
                                                                           370 |                                                        
                                                                             372

Chain C from PDB  Type:PROTEIN  Length:110
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:112
                                   326       336       346       356       366       376       386       396       406       416       426  
          TXND5_HUMAN   317 PEADKGTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
               SCOP domains d3u  vtc_ C: automated matches                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--...eee...hhhhhhh..eeeeeee...hhhhhhhhhhhhhhh..........eeeeee...hhhhhhhh......eeeeee..eeeee.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------THIOREDOXIN_1      -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.8c ---------------------------Exon 1.10  PDB: C:349-392 UniProt: 349-392  Exon 1.11c  PDB: C:393-428           Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.9  PDB: C:322-349    ------------------------------------------------------------------------------- Transcript 1 (2)
                 3uvt C 319 PLG--STVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
                              |  | 326       336       346       356       366       376       386       396       406       416       426  
                            321  |                                                                                                          
                               322

Chain D from PDB  Type:PROTEIN  Length:107
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:107
                                   331       341       351       361       371       381       391       401       411       421       
          TXND5_HUMAN   322 GTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
               SCOP domains d3uvtd_ D: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhh......eeeeee..eeeee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------THIOREDOXIN_1      -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---------------------------Exon 1.10  PDB: D:349-392 UniProt: 349-392  Exon 1.11c  PDB: D:393-428           Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: D:322-349    ------------------------------------------------------------------------------- Transcript 1 (2)
                 3uvt D 322 STVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
                                   331       341       351       361       371       381       391       401       411       421

Chain E from PDB  Type:PROTEIN  Length:96
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:105
                                   333       343       353       363       373       383       393       403       413       423     
          TXND5_HUMAN   324 VLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
               SCOP domains d3uvte_ E: automated ma      tches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....hhhhhh..eeeeee.------...hhhhhhhhhhh........eeeee---...............eeeeee..eeeee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOREDOXIN_1      -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -------------------------Exon 1.10  PDB: E:353-392 (gaps)            Exon 1.11c  PDB: E:393-428           Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: E:324-346  ------------------------------------------------------------------------------- Transcript 1 (2)
                 3uvt E 324 VLALTENNFDDTIAEGITFIKFY------CKTLAPTWEELSKKEFPGLAGVKIAEV---AERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
                                   333       343  |    353       363       373     | 383       393       403       413       423     
                                                346    353                       379 383

Legend:		→ Mismatch	(orange background)
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	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: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: automated matches (347)

Protein domain: automated matches (347)

Human (Homo sapiens) [TaxId: 9606] (87)

1a	d3uvta_	A:
1b	d3uvtb_	B:
1c	d3uvtc_	C:
1d	d3uvtd_	D:
1e	d3uvte_	E:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (TXND5_HUMAN | Q8NBS9)

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.
biological process
	GO:0043277	apoptotic cell clearance	The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic 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: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.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043202	lysosomal lumen	The volume enclosed within the lysosomal membrane.

Asymmetric Unit
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	3uvt
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	TXND5_HUMAN \| Q8NBS9	:	2diz 3uj1 3wgd 3wge 3wgx

(no "Related Entries Specified in the PDB File" available for 3UVT)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

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