1WC5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   SOLUBLE ADENYLYL CYCLASE CYAC FROM S. PLATENSIS IN COMPLEX WITH ALPHA,BETA-METHYLENE-ATP IN PRESENCE OF BICARBONATE

Authors :   C. Steegborn, T. N. Litvin, L. R. Levin, J. Buck, H. Wu

Date :   08 Nov 04 (Deposition) - 20 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Cyclase, Soluble Adenylyl Cyclase, Camp Signaling, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Steegborn, T. N. Litvin, L. R. Levin, J. Buck, H. Wu
Bicarbonate Activation Of Adenylyl Cyclase Via Promotion Of Catalytic Active Site Closure And Metal Recruitment
Nat. Struct. Mol. Biol. V. 12 32 2005
PubMed-ID: 15619637 | Reference-DOI: 10.1038/NSMB880

Molecule 1 - ADENYLATE CYCLASE
	Chains	:	A, B, C, D
	EC Number	:	4.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 1005-1202
	Organism Scientific	:	SPIRULINA PLATENSIS
	Organism Taxid	:	118562
	Synonym	:	SOLUBLE ADENYLYL CYCLASE CYAC

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	APC	4	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	CA	4	Ligand/Ion	CALCIUM ION
3	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	APC	2	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	APC	2	Ligand/Ion	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:1017 , APC A:1500 , HOH A:2010	BINDING SITE FOR RESIDUE MG A2000
02	AC2	SOFTWARE	ASP A:1017 , ILE A:1018 , ASP A:1061 , APC A:1500	BINDING SITE FOR RESIDUE CA A2100
03	AC3	SOFTWARE	ASP B:1017 , APC B:1500	BINDING SITE FOR RESIDUE MG B2000
04	AC4	SOFTWARE	ASP B:1017 , ILE B:1018 , ASP B:1061 , APC B:1500	BINDING SITE FOR RESIDUE CA B2100
05	AC5	SOFTWARE	ASP C:1017 , APC C:1500 , HOH C:2022	BINDING SITE FOR RESIDUE MG C2000
06	AC6	SOFTWARE	ASP C:1017 , ILE C:1018 , ASP C:1061 , APC C:1500	BINDING SITE FOR RESIDUE CA C2100
07	AC7	SOFTWARE	ASP D:1017 , APC D:1500	BINDING SITE FOR RESIDUE MG D2000
08	AC8	SOFTWARE	ASP D:1017 , ILE D:1018 , ASP D:1061 , APC D:1500	BINDING SITE FOR RESIDUE CA D2100
09	AC9	SOFTWARE	ASP A:1017 , ILE A:1018 , GLY A:1020 , PHE A:1021 , THR A:1022 , VAL A:1059 , GLY A:1060 , ASP A:1061 , ARG A:1117 , MG A:2000 , HOH A:2021 , CA A:2100 , LYS D:1057 , MET D:1064 , THR D:1139 , ALA D:1140 , ILE D:1141 , VAL D:1145 , ASN D:1146 , ARG D:1150 , HOH D:2012	BINDING SITE FOR RESIDUE APC A1500
10	BC1	SOFTWARE	ASP B:1017 , ILE B:1018 , VAL B:1019 , GLY B:1020 , PHE B:1021 , THR B:1022 , VAL B:1059 , GLY B:1060 , ASP B:1061 , ARG B:1117 , MG B:2000 , HOH B:2009 , CA B:2100 , PHE C:1015 , LYS C:1057 , MET C:1064 , THR C:1139 , ALA C:1140 , ILE C:1141 , VAL C:1145 , ASN C:1146 , ARG C:1150 , HOH C:2019	BINDING SITE FOR RESIDUE APC B1500
11	BC2	SOFTWARE	LYS B:1057 , MET B:1064 , THR B:1139 , ALA B:1140 , VAL B:1145 , ASN B:1146 , ALA B:1149 , ARG B:1150 , LYS B:1184 , ASP C:1017 , ILE C:1018 , VAL C:1019 , GLY C:1020 , PHE C:1021 , THR C:1022 , VAL C:1059 , GLY C:1060 , ASP C:1061 , ARG C:1117 , MG C:2000 , HOH C:2018 , HOH C:2027 , HOH C:2028 , HOH C:2029 , CA C:2100	BINDING SITE FOR RESIDUE APC C1500
12	BC3	SOFTWARE	LYS A:1057 , MET A:1064 , THR A:1139 , ALA A:1140 , ASN A:1146 , ALA A:1149 , ARG A:1150 , ASP D:1017 , ILE D:1018 , VAL D:1019 , GLY D:1020 , PHE D:1021 , THR D:1022 , VAL D:1059 , GLY D:1060 , ASP D:1061 , ARG D:1117 , MG D:2000 , HOH D:2012 , CA D:2100	BINDING SITE FOR RESIDUE APC D1500

(no "SS Bond" information available for 1WC5)

Asymmetric Unit

No.	Residues
1	Ala A:1069	-	Pro A:1070
2	Ala B:1069	-	Pro B:1070
3	Ala C:1069	-	Pro C:1070
4	Ala D:1069	-	Pro D:1070

(no "SAP(SNP)/Variant" information available for 1WC5)

(no "PROSITE Motif" information available for 1WC5)

(no "Exon" information available for 1WC5)

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:193
 aligned with O32393_ARTPT | O32393 from UniProtKB/TrEMBL  Length:1202

    Alignment length:195
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193     
        O32393_ARTPT   1004 LRPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVGRNEVPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPN 1198
               SCOP domains d1wc5a_ A: Adenylate cyclase CyaC                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....--.....eeeeeeeee.eeeeee....eeeeeehhhhhhhhhhhhhh....eeeehhhhh..hhh.eeeeeee........eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc5 A 1004 MRPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVGR--VPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPN 1198
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103    | 1113      1123      1133      1143      1153      1163      1173      1183      1193     
                                                                                                                                 1108  |                                                                                       
                                                                                                                                    1111

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with O32393_ARTPT | O32393 from UniProtKB/TrEMBL  Length:1202

    Alignment length:196
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      
        O32393_ARTPT   1004 LRPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVGRNEVPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPNM 1199
               SCOP domains d1wc5b_ B: Adenylate cyclase CyaC                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......--.....eeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhh....eeeehhhhh..hhh.eeeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc5 B 1004 MRPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVGR--VPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPNM 1199
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103    | 1113      1123      1133      1143      1153      1163      1173      1183      1193      
                                                                                                                                 1108  |                                                                                        
                                                                                                                                    1111

Chain C from PDB  Type:PROTEIN  Length:198
 aligned with O32393_ARTPT | O32393 from UniProtKB/TrEMBL  Length:1202

    Alignment length:198
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191        
        O32393_ARTPT   1002 LDLRPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVGRNEVPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPNM 1199
               SCOP domains d1wc5c_ C: Adenylate cyclase CyaC                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhh....eeeehhhhh..hhh.eeeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1wc5 C 1002 SHMRPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVGRNEVPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPNM 1199
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191

Chain D from PDB  Type:PROTEIN  Length:193
 aligned with O32393_ARTPT | O32393 from UniProtKB/TrEMBL  Length:1202

    Alignment length:195
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194     
        O32393_ARTPT   1005 RPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVGRNEVPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPNM 1199
               SCOP domains d1wc5d_ D: Adenylate cyclase CyaC                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....--......eeeeeeeeeeeeeeee....eeeeeehhhhhhhhhhhhhh...eeeeehhhhh..hhh.eeeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc5 D 1005 RPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGAPEEMSPSEQVRRAIATARQMLVALEKLNQGWQERGLVG--EVPPVRFRCGIHQGMAVVGLFGSQERSDFTAIGPSVNIAARLQEATAPNSIMVSAMVAQYVPDEEIIKREFLELKGIDEPVMTCVINPNM 1199
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104  |  |1114      1124      1134      1144      1154      1164      1174      1184      1194     
                                                                                                                               1107  |                                                                                         
                                                                                                                                  1110

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: Ferredoxin-like (1795)

Superfamily: Nucleotide cyclase (51)

Family: Adenylyl and guanylyl cyclase catalytic domain (42)

Protein domain: Adenylate cyclase CyaC (6)

Spirulina platensis [TaxId: 118562] (6)

1a	d1wc5a_	A:
1b	d1wc5b_	B:
1c	d1wc5c_	C:
1d	d1wc5d_	D:

(no "CATH Domain" information available for 1WC5)

(no "Pfam Domain" information available for 1WC5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O32393_ARTPT | O32393)

molecular function
	GO:0004016	adenylate cyclase activity	Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
	GO:0016849	phosphorus-oxygen lyase activity	Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
	GO:0016772	transferase activity, transferring phosphorus-containing groups	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
	GO:0006171	cAMP biosynthetic process	The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0009190	cyclic nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:1069 - Pro A:1070	[ RasMol ]
		Ala B:1069 - Pro B:1070	[ RasMol ]
		Ala C:1069 - Pro C:1070	[ RasMol ]
		Ala D:1069 - Pro D:1070	[ RasMol ]

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	1wc5
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	O32393_ARTPT \| O32393
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	4.6.1.1
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	O32393_ARTPT \| O32393
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UniProtKB/TrEMBL
	O32393_ARTPT \| O32393	:	1wc0 1wc1 1wc3 1wc4 1wc6 2bw7

1wc0	SOLUBLE ADENYLYL CYCLASE CYAC FROM S. PLATENSIS IN COMPLEX WITH ALPHA,BETA- METHYLENE-ATP
1wc1	SOLUBLE ADENYLYL CYCLASE CYAC FROM S. PLATENSIS IN COMPLEX WITH RP-ATPALPHAS
1wc3	SOLUBLE ADENYLYL CYCLASE CYAC FROM S. PLATENSIS IN COMPLEX WITH ALPHA,BETA- METHYLENE-ATP AND STRONTIUM
1wc4	SOLUBLE ADENYLYL CYCLASE CYAC FROM S. PLATENSIS IN COMPLEX WITH ALPHA,BETA- METHYLENE-ATP AND EUROPIUM
1wc6	SOLUBLE ADENYLYL CYCLASE CYAC FROM S. PLATENSIS IN COMPLEX WITH RP-ATPALPHAS IN PRESENCE OF BICARBONATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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