3CL1 - JenaLib

Title :   M. LOTI CYCLIC-NUCLEOTIDE BINDING DOMAIN, CYCLIC-GMP BOUND

Authors :   G. M. Clayton, S. L. Alteiri, L. R. Thomas, J. H. Morais-Cabral

Date :   18 Mar 08 (Deposition) - 05 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Cyclic-Nucleotide Binding, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. L. Altieri, G. M. Clayton, W. R. Silverman, A. O. Olivares, E. M. De La Cruz, L. R. Thomas, J. H. Morais-Cabral
Structural And Energetic Analysis Of Activation By A Cyclic Nucleotide Binding Domain.
J. Mol. Biol. V. 381 655 2008
PubMed-ID: 18619611 | Reference-DOI: 10.1016/J.JMB.2008.06.011
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CNGK1_RHILO	235-348	2	A:235-348 B:235-348
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CNGK1_RHILO	262-278	2	A:262-278 B:262-278
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CNGK1_RHILO	296-313	2	A:296-313 B:296-313

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CNGK1_RHILO	235-348	2	A:235-348 B:235-348
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CNGK1_RHILO	262-278	2	A:262-278 B:262-278
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CNGK1_RHILO	296-313	2	A:296-313 B:296-313

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CNGK1_RHILO	235-348	2	A:235-348 B:235-348
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CNGK1_RHILO	262-278	2	A:262-278 B:262-278
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CNGK1_RHILO	296-313	2	A:296-313 B:296-313

Exons (0, 0)

Sequences/Alignments

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:130
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:130
                                   229       239       249       259       269       279       289       299       309       319       329       339       349
          CNGK1_RHILO   220 RGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERR 349
               SCOP domains d3cl1a_ A: automated matches                                                                                                       SCOP domains
               CATH domains 3cl1A00 A:220-349 Jelly Rolls                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eee.......eeeeeee..eee.....eee....eehhhhhhhh......eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------CNMP_BINDING_3  PDB: A:235-348 UniProt: 235-348                                                                   - PROSITE (1)
                PROSITE (2) ------------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cl1 A 220 RGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERR 349
                                   229       239       249       259       269       279       289       299       309       319       329       339       349

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with CNGK1_RHILO | Q98GN8 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:131
                                   228       238       248       258       268       278       288       298       308       318       328       338       348 
          CNGK1_RHILO   219 RRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERR 349
               SCOP domains d3cl1b_ B: automated matches                                                                                                        SCOP domains
               CATH domains 3cl1B00 B:219-349 Jelly Rolls                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eee.......eeeeeee..eee.....eee....eehhhhhhhh......eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------CNMP_BINDING_3  PDB: B:235-348 UniProt: 235-348                                                                   - PROSITE (1)
                PROSITE (2) -------------------------------------------CNMP_BINDING_1   -----------------CNMP_BINDING_2    ------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cl1 B 219 RRGDFVRNWQLVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPVELGPGAFFGEMALISGEPRSATVSAATTVSLLSLHSADFQMLCSSSPEIAEIFRKTALERR 349
                                   228       238       248       258       268       278       288       298       308       318       328       338       348

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CNGK1_RHILO | Q98GN8)

molecular function
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005267	potassium channel activity	Enables the facilitated diffusion of a potassium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005249	voltage-gated potassium channel activity	Enables the transmembrane transfer of a potassium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071805	potassium ion transmembrane transport	A process in which a potassium ion is transported from one side of a membrane to the other.
	GO:0006813	potassium ion transport	The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	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.
	GO:0008076	voltage-gated potassium channel complex	A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PCG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		POL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3cl1)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3cl1
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CNGK1_RHILO \| Q98GN8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description