1TX5 - JenaLib

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Theoretical Model (Jmol Viewer)

Title :   MOLECULAR ANALYSIS OF INTERACTION BETWEEN ANTHRAX TOXIN RECEPTOR AND PROTECTIVE ANTIGEN

Authors :   J. Pandey, D. Warburton

Date :   01 Jul 04 (Deposition) - 22 Nov 05 (Release) - 22 Nov 05 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,C,_^#
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Protective Antigen; Anthrax Toxin Receptor; Soft Docking; Bigger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Pandey, D. Warburton
Molecular Analysis Of Interaction Between Anthrax Toxin Receptor And Protective Antigen
To Be Published 2004
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTECTIVE ANTIGEN
	Chains	:	C
	Organism Common	:	BACTERIA
	Organism Scientific	:	BACILLUS ANTHRACIS
	Other Details	:	TAKEN FROM PDB ID: 1ACC

Molecule 2 - ANTHRAX TOXIN RECEPTOR 2
	Chains	:	A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Other Details	:	TAKEN FROM PDB ID: 1SHT
	Synonym	:	CAPILLARY MORPHOGENESIS PROTEIN 2


Theoretical Model	:

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Theoretical Model (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	MG	1	Ligand/Ion	MAGNESIUM ION

(no "Site" information available for 1TX5)

(no "SS Bond" information available for 1TX5)

Theoretical Model

No.	Residues
1	Tyr C:411	-	Pro C:412

Theoretical Model (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022687	L	45	P	ANTR2_HUMAN	Disease (HFS)	---	A	L	45	P
2	UniProt	VAR_022688	G	105	D	ANTR2_HUMAN	Disease (HFS)	137852902	A	G	105	D
3	UniProt	VAR_022689	I	189	T	ANTR2_HUMAN	Disease (HFS)	137852905	A	I	189	T
4	UniProt	VAR_PAG_BACAN_001 *	M	295	I	PAG_BACAN	---	---	C	M	266	I
5	UniProt	VAR_PAG_BACAN_002 *	N	392	D	PAG_BACAN	---	---	C	N	363	D
6	UniProt	VAR_PAG_BACAN_003 *	F	560	L	PAG_BACAN	---	---	C	F	531	L
7	UniProt	VAR_PAG_BACAN_004 *	P	565	S	PAG_BACAN	---	---	C	P	536	S
8	UniProt	VAR_PAG_BACAN_005 *	A	600	V	PAG_BACAN	---	---	C	A	571	V
	* ID not provided by source

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

Theoretical Model (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA14	PS51820	PA14 domain profile.	PAG_BACAN	43-179	1	C:14-150
2	VWFA	PS50234	VWFA domain profile.	ANTR2_HUMAN	44-213	1	A:44-213

Theoretical Model (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.8d	ENST00000307333	8d	ENSE00001871464	chr4:80993717-80993563	155	ANTR2_HUMAN	1-51	51	1	A:41-51	11
1.9a	ENST00000307333	9a	ENSE00001761580	chr4:80992808-80992737	72	ANTR2_HUMAN	51-75	25	1	A:51-75	25
1.10	ENST00000307333	10	ENSE00001798474	chr4:80990661-80990590	72	ANTR2_HUMAN	75-99	25	1	A:75-99	25
1.11	ENST00000307333	11	ENSE00001123454	chr4:80977167-80977086	82	ANTR2_HUMAN	99-126	28	1	A:99-126	28
1.12	ENST00000307333	12	ENSE00001123446	chr4:80976621-80976514	108	ANTR2_HUMAN	127-162	36	1	A:127-162	36
1.13	ENST00000307333	13	ENSE00001123438	chr4:80976372-80976304	69	ANTR2_HUMAN	163-185	23	1	A:163-185	23
1.14b	ENST00000307333	14b	ENSE00001123430	chr4:80975506-80975426	81	ANTR2_HUMAN	186-212	27	1	A:186-212	27
1.15	ENST00000307333	15	ENSE00001123421	chr4:80957186-80957126	61	ANTR2_HUMAN	213-233	21	1	A:213-217	5
1.16	ENST00000307333	16	ENSE00001123410	chr4:80954724-80954626	99	ANTR2_HUMAN	233-266	34	0	-	-
1.17	ENST00000307333	17	ENSE00001123400	chr4:80952846-80952777	70	ANTR2_HUMAN	266-289	24	0	-	-
1.19	ENST00000307333	19	ENSE00001712373	chr4:80940130-80940052	79	ANTR2_HUMAN	289-315	27	0	-	-
1.20	ENST00000307333	20	ENSE00001665059	chr4:80929770-80929675	96	ANTR2_HUMAN	316-347	32	0	-	-
1.21	ENST00000307333	21	ENSE00001771910	chr4:80906017-80905973	45	ANTR2_HUMAN	348-362	15	0	-	-
1.22	ENST00000307333	22	ENSE00001710470	chr4:80905124-80905032	93	ANTR2_HUMAN	363-393	31	0	-	-
1.23	ENST00000307333	23	ENSE00001599114	chr4:80899328-80899161	168	ANTR2_HUMAN	394-449	56	0	-	-
1.24b	ENST00000307333	24b	ENSE00001257764	chr4:80898855-80898733	123	ANTR2_HUMAN	450-489	40	0	-	-

Theoretical Model

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:177
 aligned with ANTR2_HUMAN | P58335 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:177
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
          ANTR2_HUMAN    41 RAFDLYFVLDKSGSVANNWIEIYNFVQQLAERFVSPEMRLSFIVFSSQATIILPLTGDRGKISKGLEDLKRVSPVGETYIHEGLKLANEQIQKAGGLKTSSIIIALTDGKLDGLVPSYAEKEAKISRSLGASVYCVGVLDFEQAQLERIADSKEQVFPVKGGFQALKGIINSILAQS 217
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eeeeeeee.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhheeeeeeee......hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh.hhh.eee.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----P-----------------------------------------------------------D-----------------------------------------------------------------------------------T---------------------------- SAPs(SNPs)
                PROSITE (2) ---VWFA  PDB: A:44-213 UniProt: 44-213                                                                                                                                       ---- PROSITE (2)
           Transcript 1 (1) Exon 1.8d  -----------------------Exon 1.10  PDB: A:75-99  ---------------------------Exon 1.12  PDB: A:127-162           Exon 1.13              Exon 1.14b  PDB: A:186-212 1.15  Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.9a  PDB: A:51-75  -----------------------Exon 1.11  PDB: A:99-126    ------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1tx5 A  41 RAFDLYFVLDKSGSVANNWIEIYNFVQQLAERFVSPEMRLSFIVFSSQATIILPLTGDRGKISKGLEDLKRVSPVGETYIHEGLKLANEQIQKAGGLKTSSIIIALTDGKLDGLVPSYAEKEAKISRSLGASVYCVGVLDFEQAQLERIADSKEQVFPVKGGFQALKGIINSILAQS 217
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:665
 aligned with PAG_BACAN | P13423 from UniProtKB/Swiss-Prot  Length:764

    Alignment length:722
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762  
            PAG_BACAN    43 SSSQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSELENIPSENQYFQSAIWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASNSNKIRLEKGRLYQIKIQYQRENPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQKSSNSRKKRSTSAGPTVPDRDNDGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWSTASDPYSDFEKVTGRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTSRTHTSEVHGNAEVHASFFDIGGSVSAGFSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARLNANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEPNGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDRNNIAVGADESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEIG 764
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.......eeeeee........hhhhh...hhhhhh..eeeeeeeee....eeeeeee.hhh.eeeee..eeee.----...eee....eeeeeeeee............eeee.....eee.....ee.........-------------.........hhhhhhhheeeee....eeeee.hhhhhhh....................hhhhhhhh......hhhhhh........eeeeeeeeeeee..------------.eeeeeeeee......----------------........eeeeeee........--------.......eeeeeeeeeee............eeeee...eeeeee..............eee.......ee...........eeehhhhhhhhhhhheeeeee.....eeeeee....eeeeeeeeehhhhhhhhhhheeeeee.......eeeeee.....----......hhhhhhhhhhh........ee..ee...eeeeehhhhhhhhhhhhhhhh...hhhhh.........eeeeee...ee.....eee.hhhhhhhh...eeee...eeee..hhhhhhheeeeeeeee.....eee..........eee.....eeee.................eeeeeeee.hhh.................eeeeeeehhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------D-----------------------------------------------------------------------------------------------------------------------------------------------------------------------L----S----------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PA14  PDB: C:14-150 UniProt: 43-179                                                                                                      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tx5 C  14 SSSQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSELENIPSENQYFQSAIWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVIN----SNKIRLEKGRLYQIKIQYQRENPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQKSS-------------VPDRDNDGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWSTASDPYSDFEKVTGRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNE------------TISKNTSTSRTHTSEV----------------VSAGFSNSNSSTVAIDHSLSLAG--------GLNTADTARLNANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPS----TTKPDMTLKEALKIAFGFNEPNGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDRNNIAVGADESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEIG 735
                                    23        33        43        53        63        73        83        93    |  103       113       123       133       143       153       | -         - |     183       193       203       213       223       233       243       253       263       273 |       -    |  293       303         -      |323       333        |-       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       | -  |    523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733  
                                                                                                               98  103                                                       161           175                                                                                                 275          288            303              320                   342      351                                                                                                                                                             511  516

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 1TX5)

(no "CATH Domain" information available for 1TX5)

(no "Pfam Domain" information available for 1TX5)

Theoretical Model(hide GO term definitions)

Chain A (ANTR2_HUMAN | P58335)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0022414	reproductive process	A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
	GO:1901998	toxin transport	The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C (PAG_BACAN | P13423)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0043409	negative regulation of MAPK cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0001933	negative regulation of protein phosphorylation	Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0044533	positive regulation of apoptotic process in other organism	Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism.
	GO:0097300	programmed necrotic cell death	A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0035897	proteolysis in other organism	The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds.
	GO:1903140	regulation of establishment of endothelial barrier	Any process that modulates the frequency, rate or extent of establishment of endothelial barrier.
	GO:0061136	regulation of proteasomal protein catabolic process	Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
cellular component
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Theoretical Model
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	Cis Peptide Bonds
		Tyr C:411 - Pro C:412	[ RasMol ]

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1pqb	ANALYSIS OF BINDING BETWEEN ANTHRAX PROTECTIVE ANTIGEN AND VWA/I DOMAIN OF INTEGRINS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 8)

PROSITE Motifs (2, 2)

Exons (8, 8)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (27, 32)

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Related Entries Specified in the PDB File