1CYN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CYCLOPHILIN B COMPLEXED WITH [D-(CHOLINYLESTER)SER8]-CYCLOSPORIN

Authors :   V. Mikol, J. Kallen, M. D. Walkinshaw

Date :   22 May 95 (Deposition) - 29 Jan 96 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A,C

Keywords :   Isomerase-Immunosuppressant Complex, Cyclosporin, Isomerase, Rotamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Mikol, J. Kallen, M. D. Walkinshaw
X-Ray Structure Of A Cyclophilin B/Cyclosporin Complex: Comparison With Cyclophilin A And Delineation Of Its Calcineurin-Binding Domain.
Proc. Natl. Acad. Sci. Usa V. 91 5183 1994
PubMed-ID: 8197205 | Reference-DOI: 10.1073/PNAS.91.11.5183
(for further references see the PDB file header)

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B
	Chains	:	A
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	CYCLOPHILIN
	Expression System Taxid	:	562
	Gene	:	CYCLOPHILIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PPIASE B, ROTAMASE B, CYCLOPHILIN B

Molecule 2 - CYCLOSPORIN A
	Chains	:	C
	Engineered	:	YES
	Organism Scientific	:	TOLYPOCLADIUM INFLATUM
	Organism Taxid	:	29910
	Other Details	:	D-(CHOLINYL)SER AT POSITION 1
	Synonym	:	CYCLOSPORINE, CICLOSPORIN, CICLOSPORINE
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 9)

No.	Name	Count	Type	Full Name
1	ABA	1	Mod. Amino Acid	ALPHA-AMINOBUTYRIC ACID
2	BMT	1	Mod. Amino Acid	4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
3	DSN	1	Mod. Amino Acid	D-SERINE
4	MLE	4	Mod. Amino Acid	N-METHYLLEUCINE
5	MVA	1	Mod. Amino Acid	N-METHYLVALINE
6	SAR	1	Mod. Amino Acid	SARCOSINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:63 , PHE A:68 , GLN A:71 , GLY A:80 , ALA A:109 , ASN A:110 , ALA A:111 , GLN A:119 , PHE A:121 , TRP A:129 , HIS A:134 , HOH C:2001 , HOH C:2002 , HOH C:2004 , HOH C:2006 , HOH C:2007	BINDING SITE FOR CHAIN C OF CYCLOSPORIN A

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

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

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047711	V	60	L	PPIB_HUMAN	Polymorphism	11558595	A	V	28	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CSA_PPIASE_2	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.	PPIB_HUMAN	47-204	1	A:15-172
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	PPIB_HUMAN	88-105	1	A:56-73

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000300026	1	ENSE00001201753	chr15:64455404-64455051	354	PPIB_HUMAN	1-45	45	1	A:7-13	7
1.2	ENST00000300026	2	ENSE00001106698	chr15:64454353-64454240	114	PPIB_HUMAN	46-83	38	1	A:14-51	38
1.3	ENST00000300026	3	ENSE00001106705	chr15:64452396-64452303	94	PPIB_HUMAN	84-115	32	1	A:52-83	32
1.4	ENST00000300026	4	ENSE00001106702	chr15:64449108-64448924	185	PPIB_HUMAN	115-176	62	1	A:83-144	62
1.5	ENST00000300026	5	ENSE00001201748	chr15:64448344-64448011	334	PPIB_HUMAN	177-216	40	1	A:145-184	40

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:178
 aligned with PPIB_HUMAN | P23284 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:178
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
           PPIB_HUMAN    39 GPKVTVKVYFDLRIGDEDVGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTAWLDGKHVVFGKVLEGMEVVRKVESTKTDSRDKPLKDVIIADCGKIEVEKPFAIAKE 216
               SCOP domains d1cyna_ A: Cyclophilin (eukaryotic)                                                                                                                                                SCOP domains
               CATH domains 1cynA00 A:7-184 Cyclophilin                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh............eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------L------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------CSA_PPIASE_2  PDB: A:15-172 UniProt: 47-204                                                                                                                   ------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------CSA_PPIASE_1      --------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1    Exon 1.2  PDB: A:14-51 UniProt: 46-83 Exon 1.3  PDB: A:52-83          -------------------------------------------------------------Exon 1.5  PDB: A:145-184                 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.4  PDB: A:83-144 UniProt: 115-176                      ---------------------------------------- Transcript 1 (2)
                 1cyn A   7 GPKVTVKVYFDLRIGDEDVGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGERFPDENFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTAWLDGKHVVFGKVLEGMEVVRKVESTKTDSRDKPLKDVIIADCGKIEVEKPFAIAKE 184
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1cyn C   1 xxxxxxxxVxA  11
                            ||||||||10 
                            1-DSN||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE
                                    10-MLE

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Cyclophilin-like (169)

Superfamily: Cyclophilin-like (169)

Family: Cyclophilin (peptidylprolyl isomerase) (160)

Protein domain: Cyclophilin (eukaryotic) (77)

Human (Homo sapiens), variant B [TaxId: 9606] (1)

d1cyna_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cyclophilin (95)

Homologous Superfamily: Cyclophilin (95)

Human (Homo sapiens) (58)

1cynA00

A:7-184

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PPIB_HUMAN | P23284)

molecular function
	GO:0070063	RNA polymerase binding	Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
	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:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	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).
	GO:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0060348	bone development	The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
	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:0044829	positive regulation by host of viral genome replication	A process in which a host organism activates or increases the frequency, rate or extent of viral genome replication.
	GO:0044794	positive regulation by host of viral process	A process in which a host organism activates or increases the frequency, rate or extent of the release of a process being mediated by a virus with which it is infected.
	GO:0040018	positive regulation of multicellular organism growth	Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
	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.
	GO:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
	GO:1901873	regulation of post-translational protein modification	Any process that modulates the frequency, rate or extent of post-translational protein modification.
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:0034663	endoplasmic reticulum chaperone complex	A protein complex that is located in the endoplasmic reticulum and is composed of chaperone proteins, including BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1.
	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:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0032991	macromolecular complex	A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
	GO:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005790	smooth endoplasmic reticulum	The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cyn)

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	1cyn
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	PPIB_HUMAN \| P23284	:	3ich 3ici

1bck	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN C
1c5f	CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A
1csa	SOLUTION STRUCTURE OF E.COLI CYCLOPHILIN (F112W) COMPLEXED WITH CYCLOSPORIN A
1cwa	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
1cwb	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 5
1cwc	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwf	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN D
1cwh	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A MODIFIED AT POSITION 7
1cwi	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITION 7
1cwj	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITIONS 5 AND 7.
1cwk	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITIONS 5 AND 7.
1cwl	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwm	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwo	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH NODIFIED CYCLOSPORIN C AT POSITIONS 1, AND 9
1cya	SOLUTION STRUCTURE OF HUMAN CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1cyb	SOLUTION STRUCTURE OF HUMAN CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1ikf	CRYSTAL STRUCTURE OF CTCLOSPORIN-FAB COMPLEX
1m63	CRYSTAL STRUCTURE OF CALCINEURIN-CYCLOPHILIN-CYCLOSPORIN COMPLEX
1mf8	CRYSTAL STRUCTURE OF HUMAN CALCINEURIN COMPLEXED WITH HUMAN CYCLOPHILIN AND CYCLOSPORIN A
1mik	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 6
1qng	CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1qnh	CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM CYCLOPHILIN (DOUBLE MUTANT) COMPLEXED WITH CYCLOSPORIN A
1xq7	CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
2esl	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN C COMPLEXED WITH CYCLOSPORIN A
2oju	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN J COMPLEXED WITH CYCLOSPORIN A
2poy	CRYSTAL STRUCTURE OF CRYPTOSPORIDIUM PARVUM IOWA II CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
2rma	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
2rmb	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 5
2rmc	CRYSTAL STRUCTURE OF MURINE CYCLOPHILIN C COMPLEXED WITH CYCLOSPORIN A
2wfj	CRYSTAL STRUCTURE OF THE PPIASE DOMAIN OF HUMAN CYCLOPHILIN G COMPLEXED WITH CYCLOSPORIN A
2x2c	CRYSTAL STRUCTURE OF HUMAN ACETYL-CYPA COMPLEXED WITH CYCLOSPORINE A
2x7k	CRYSTAL STRUCTURE OF PPIL1 COMPLEXED WITH CYCLOSPORINE A
2z6w	CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN D IN COMPLEX WITH CYCLOSPORIN A
3bo7	CRYSTAL STRUCTURE OF CYCLOSPHILIN A FROM TOXOPLASMA GONDII COMPLEXED WIT CYCLOSPORIN A
3cys	SOLUTION STRUCTURE OF THE HUMAN CYCLOSPORIN A COMPLEXED WITH CYCLOSPORIN A
3eov	CRYSTAL STRUCTURE OF CYCLOPHILIN FROM LEISHMANIA DONOVANI COMPLEXED WITH CYCLOSPORIN A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 9)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (5, 5)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (28, 28)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File