1NYA - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   NMR SOLUTION STRUCTURE OF CALERYTHRIN, AN EF-HAND CALCIUM-BINDING PROTEIN

Authors :   H. Tossavainen, P. Permi, A. Annila, I. Kilpelainen, T. Drakenberg

Date :   12 Feb 03 (Deposition) - 05 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Ef-Hand, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Tossavainen, P. Permi, A. Annila, I. Kilpelainen, T. Drakenberg
Nmr Solution Structure Of Calerythrin, An Ef-Hand Calcium-Binding Protein From Saccharopolyspora Erythraea
Eur. J. Biochem. V. 270 2505 2003
PubMed-ID: 12755706 | Reference-DOI: 10.1046/J.1432-1033.2003.03623.X
(for further references see the PDB file header)

Molecule 1 - CALERYTHRIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	SACCHAROPOLYSPORA ERYTHRAEA
	Organism Taxid	:	1836
	Synonym	:	CALCIUM-BINDING PROTEIN


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 3)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION

NMR Structure (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:17 , PHE A:18 , ASP A:19 , ASN A:21 , ALA A:23 , ASP A:28	BINDING SITE FOR RESIDUE CA A 500
2	AC2	SOFTWARE	ASP A:112 , ASN A:114 , ASP A:116 , GLN A:118 , GLU A:123	BINDING SITE FOR RESIDUE CA A 501
3	AC3	SOFTWARE	ASP A:146 , THR A:147 , ASN A:148 , ASN A:150 , GLU A:152 , GLU A:157	BINDING SITE FOR RESIDUE CA A 502

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

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

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

NMR Structure (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CBP_SACER	5-40 134-169 100-133	3	A:4-39 A:133-168 A:99-132
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CBP_SACER	18-30 113-125 147-159	3	A:17-29 A:112-124 A:146-158

(no "Exon" information available for 1NYA)

NMR Structure

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:176
 aligned with CBP_SACER | P06495 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      
            CBP_SACER     2 TTAIASDRLKKRFDRWDFDGNGALERADFEKEAQHIAEAFGKDAGAAEVQTLKNAFGGLFDYLAKEAGVGSDGSLTEEQFIRVTENLIFEQGEASFNRVLGPVVKGTWGMCDKNADGQINADEFAAWLTALGMSKAEAAEAFNQVDTNGNGELSLDELLTAVRDFHFGRLDVELLG 177
               SCOP domains d1nyaa_ A: Calerythrin                                                                                                                                                           SCOP domains
               CATH domains 1nyaA00 A:1-176 EF-hand                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------efhand-1nyaA01 A:137-165     ----------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhh..hhhhhhhhhhhhh.....eeehhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---EF_HAND_2  PDB: A:4-39 UniProt: 5-40-----------------------------------------------------------EF_HAND_2  PDB: A:99-132          EF_HAND_2  PDB: A:133-168           -------- PROSITE (1)
                PROSITE (2) ----------------EF_HAND_1    ----------------------------------------------------------------------------------EF_HAND_1    ---------------------EF_HAND_1    ------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nya A   1 TTAIASDRLKKRFDRWDFDGNGALERADFEKEAQHIAEAFGKDAGAAEVQTLKNAFGGLFDYLAKEAGVGSDGSLTEEQFIRVTENLIFEQGEASFNRVLGPVVKGIVGMCDKNADGQINADEFAAWLTALGMSKAEAAEAFNQVDTNGNGELSLDELLTAVRDFHFGRLDVELLG 176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Calerythrin (1)

Saccharopolyspora erythraea [TaxId: 1836] (1)

d1nyaa_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Saccharopolyspora erythraea. Organism_taxid: 1836. (1)

1nyaA00

A:1-176

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: efhand (70)

Saccharopolyspora erythraea (Streptomyces erythraeus) (1)

efhand-1nyaA01

A:137-165

NMR Structure(hide GO term definitions)

Chain A (CBP_SACER | P06495)

molecular function
	GO:0005509		calcium ion binding		Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

NMR Structure
	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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - model 1, sites PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1nya
		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
	CBP_SACER \| P06495
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CBP_SACER \| P06495
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1NYA)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (2, 2)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File