1U79 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

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Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ATFKBP13

Authors :   G. Gopalan, K. Swaminathan

Date :   03 Aug 04 (Deposition) - 28 Sep 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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)
Biol. Unit 6: A (2x),B (2x),C (2x),D (2x),E (2x)

Keywords :   Tfkbp13, Fk-506 Binding Protein, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Gopalan, Z. He, Y. Balmer, P. Romano, R. Gupta, B. B. Buchanan, K. Swaminathan, S. Luan
Structural Analysis Uncovers A Role For Redox In Regulating Fkbp13, An Immunophilin Of The Chloroplast Thylakoid Lumen
Proc. Natl. Acad. Sci. Usa V. 101 13945 2004
PubMed-ID: 15356344 | Reference-DOI: 10.1073/PNAS.0405240101
(for further references see the PDB file header)

Molecule 1 - FKBP-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 3
	Chains	:	A, B, C, D, E
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-KG
	Expression System Strain	:	BL21(DE3)LYS-S
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ATFKBP13
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	ATFKBP13, PPIASE, ROTAMASE, FK506 BINDING PROTEIN 1

		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
Biological Unit 6 (2x)	:	A (2x)	B (2x)	C (2x)	D (2x)	E (2x)

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1U79)

(no "Site" information available for 1U79)

Asymmetric Unit

No.	Residues
1	A:5	-	A:17
2	A:106	-	A:111
3	B:5	-	B:17
4	B:106	-	B:111
5	C:5	-	C:17
6	C:106	-	C:111
7	D:5	-	D:17
8	D:106	-	D:111
9	E:5	-	E:17
10	E:106	-	E:111

(no "Cis Peptide Bond" information available for 1U79)

(no "SAP(SNP)/Variant" information available for 1U79)

Asymmetric Unit (1, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	FKB13_ARATH	109-208	5	A:30-129 B:30-129 C:30-129 D:30-129 E:30-129

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	FKB13_ARATH	109-208	1	A:30-129 - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	FKB13_ARATH	109-208	1	- B:30-129 - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	FKB13_ARATH	109-208	1	- - C:30-129 - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	FKB13_ARATH	109-208	1	- - - D:30-129 -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	FKB13_ARATH	109-208	1	- - - - E:30-129

Biological Unit 6 (1, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	FKB13_ARATH	109-208	10	A:30-129 B:30-129 C:30-129 D:30-129 E:30-129

(no "Exon" information available for 1U79)

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:125
 aligned with FKB13_ARATH | Q9SCY2 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:125
                                    93       103       113       123       133       143       153       163       173       183       193       203     
          FKB13_ARATH    84 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 208
               SCOP domains d1u79a_ A: FKBP13                                                                                                             SCOP domains
               CATH domains 1u79A00 A:5-129  [code=3.10.50.40, no name defined]                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee...........eeeeeeeee.....eeeehhhhh..eeee......hhhhhhhhhh...........eeeeeehhhhh.....eeee..eeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: A:30-129 UniProt: 109-208                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u79 A   5 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 129
                                    14        24        34        44        54        64        74        84        94       104       114       124

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with FKB13_ARATH | Q9SCY2 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:125
                                    93       103       113       123       133       143       153       163       173       183       193       203     
          FKB13_ARATH    84 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 208
               SCOP domains d1u79b_ B: FKBP13                                                                                                             SCOP domains
               CATH domains 1u79B00 B:5-129  [code=3.10.50.40, no name defined]                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee...........eeeeeeeee.....eeeehhhhh..eeee......hhhhhhhhhh...........eeeeeehhhhh.....eee....eee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: B:30-129 UniProt: 109-208                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u79 B   5 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 129
                                    14        24        34        44        54        64        74        84        94       104       114       124

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with FKB13_ARATH | Q9SCY2 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:125
                                    93       103       113       123       133       143       153       163       173       183       193       203     
          FKB13_ARATH    84 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 208
               SCOP domains d1u79c_ C: FKBP13                                                                                                             SCOP domains
               CATH domains 1u79C00 C:5-129  [code=3.10.50.40, no name defined]                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee...........eeeeeeeeee....eeeehhhhh..eeee......hhhhhhhhh............eeeeeehhhhh....................eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: C:30-129 UniProt: 109-208                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u79 C   5 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 129
                                    14        24        34        44        54        64        74        84        94       104       114       124

Chain D from PDB  Type:PROTEIN  Length:125
 aligned with FKB13_ARATH | Q9SCY2 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:125
                                    93       103       113       123       133       143       153       163       173       183       193       203     
          FKB13_ARATH    84 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 208
               SCOP domains d1u79d_ D: FKBP13                                                                                                             SCOP domains
               CATH domains 1u79D00 D:5-129  [code=3.10.50.40, no name defined]                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee...........eeeeeeeeee....eeeehhhhh..eeee......hhhhhhhhhh...........eeeeeehhhhh.....eeee..eeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: D:30-129 UniProt: 109-208                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u79 D   5 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 129
                                    14        24        34        44        54        64        74        84        94       104       114       124

Chain E from PDB  Type:PROTEIN  Length:125
 aligned with FKB13_ARATH | Q9SCY2 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:125
                                    93       103       113       123       133       143       153       163       173       183       193       203     
          FKB13_ARATH    84 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 208
               SCOP domains d1u79e_ E: FKBP13                                                                                                             SCOP domains
               CATH domains 1u79E00 E:5-129  [code=3.10.50.40, no name defined]                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee...........eeeeeeeeee....eeeehhhhh..eeee......hhhhhhhhhh...........eeeeeehhhhh....................eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------FKBP_PPIASE  PDB: E:30-129 UniProt: 109-208                                                          PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u79 E   5 CEFSVSPSGLAFCDKVVGYGPEAVKGQLIKAHYVGKLENGKVFDSSYNRGKPLTFRIGVGEVIKGWDQGILGSDGIPPMLTGGKRTLRIPPELAYGDRGAGCKGGSCLIPPASVLLFDIEYIGKA 129
                                    14        24        34        44        54        64        74        84        94       104       114       124

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: FKBP-like (309)

Superfamily: FKBP-like (198)

Family: FKBP immunophilin/proline isomerase (153)

Protein domain: FKBP13 (2)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (2)

1a	d1u79a_	A:
1b	d1u79b_	B:
1c	d1u79c_	C:
1d	d1u79d_	D:
1e	d1u79e_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

Homologous Superfamily: [code=3.10.50.40, no name defined] (98)

Thale cress (Arabidopsis thaliana) (3)

1a	1u79A00	A:5-129
1b	1u79B00	B:5-129
1c	1u79C00	C:5-129
1d	1u79D00	D:5-129
1e	1u79E00	E:5-129

(no "Pfam Domain" information available for 1U79)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (FKB13_ARATH | Q9SCY2)

molecular function
	GO:0005528	FK506 binding	Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506.
	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:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
	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).
biological process
	GO:0061077	chaperone-mediated protein folding	The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
	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:0000413	protein peptidyl-prolyl isomerization	The modification of a protein by cis-trans isomerization of a proline residue.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009543	chloroplast thylakoid lumen	The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
	GO:0031977	thylakoid lumen	The volume enclosed by a thylakoid membrane.

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(no "Cis Peptide Bonds" information available for 1u79)

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	1u79
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(no "Related Entries Specified in the PDB File" available for 1U79)

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SS Bonds (10, 10)

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