1N0Y - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PB-BOUND CALMODULIN

Authors :   M. A. Wilson, A. T. Brunger

Date :   15 Oct 02 (Deposition) - 30 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Calmodulin, Lead, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Wilson, A. T. Brunger
Domain Flexibility In The 1. 75 A Resolution Structure Of Pb2+-Calmodulin.
Acta Crystallogr. , Sect. D V. 59 1782 2003
PubMed-ID: 14501118 | Reference-DOI: 10.1107/S0907444903016846

Molecule 1 - CALMODULIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK233-3
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CAM
	Organism Scientific	:	PARAMECIUM TETRAURELIA
	Organism Taxid	:	5888

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CAC	1	Ligand/Ion	CACODYLATE ION
3	PB	14	Ligand/Ion	LEAD (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	CAC	1	Ligand/Ion	CACODYLATE ION
3	PB	-1	Ligand/Ion	LEAD (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CAC	-1	Ligand/Ion	CACODYLATE ION
3	PB	-1	Ligand/Ion	LEAD (II) ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:58 , ASP A:64 , GLU A:67 , GLU B:114	BINDING SITE FOR RESIDUE PB A 500
02	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , ASP A:64 , GLU A:67	BINDING SITE FOR RESIDUE PB A 501
03	AC3	SOFTWARE	GLU A:7 , ASP A:58 , GLU B:114 , LYS B:115 , GLU B:120	BINDING SITE FOR RESIDUE PB A 502
04	AC4	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31 , HOH A:1006	BINDING SITE FOR RESIDUE PB A 503
05	AC5	SOFTWARE	GLU A:11 , GLU A:14	BINDING SITE FOR RESIDUE PB A 504
06	AC6	SOFTWARE	GLU A:2 , HOH A:1031 , GLU B:84 , GLU B:87 , GLU B:123 , HOH B:2052	BINDING SITE FOR RESIDUE PB B 505
07	AC7	SOFTWARE	CAC A:1001 , ASP B:80 , GLU B:83 , GLU B:127	BINDING SITE FOR RESIDUE PB B 506
08	AC8	SOFTWARE	GLU A:2 , CAC A:1001 , HOH A:1020 , GLU B:83 , GLU B:84 , GLU B:123 , GLU B:127	BINDING SITE FOR RESIDUE PB A 507
09	AC9	SOFTWARE	ASP B:129 , ASP B:131 , ASP B:133 , HIS B:135 , GLU B:140 , HOH B:2027	BINDING SITE FOR RESIDUE PB B 508
10	BC1	SOFTWARE	CAC A:1001 , ASP B:80 , HOH B:2041	BINDING SITE FOR RESIDUE PB B 509
11	BC2	SOFTWARE	ASP B:93 , ASP B:95 , ASN B:97 , LEU B:99 , GLU B:104 , HOH B:2050	BINDING SITE FOR RESIDUE PB B 510
12	BC3	SOFTWARE	ALA A:1 , GLU A:2 , PB A:507 , HOH A:1020 , HOH A:1034 , ASP B:80 , GLU B:83 , GLU B:127 , PB B:506 , PB B:509	BINDING SITE FOR RESIDUE CAC A 1001
13	BC4	SOFTWARE	VAL B:108 , ASN B:111 , LEU B:112	BINDING SITE FOR RESIDUE ACT B 2001

(no "SS Bond" information available for 1N0Y)

(no "Cis Peptide Bond" information available for 1N0Y)

(no "SAP(SNP)/Variant" information available for 1N0Y)

Asymmetric Unit (2, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM_PARTE	8-43 44-79 81-116 117-149	5	A:7-42 A:43-78 A:80-87 B:80-115 B:116-147
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM_PARTE	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 B:93-105 B:129-141

Biological Unit 1 (2, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM_PARTE	8-43 44-79 81-116 117-149	3	A:7-42 A:43-78 A:80-87 - -
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM_PARTE	21-33 57-69 94-106 130-142	2	A:20-32 A:56-68 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM_PARTE	8-43 44-79 81-116 117-149	2	- - - B:80-115 B:116-147
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM_PARTE	21-33 57-69 94-106 130-142	2	- - B:93-105 B:129-141

(no "Exon" information available for 1N0Y)

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:87
 aligned with CALM_PARTE | P07463 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:87
                                    11        21        31        41        51        61        71        81       
           CALM_PARTE     2 AEQLTEEQIAEFKEAFALFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLSLMARKMKEQDSEEELIE  88
               SCOP domains d1n0ya_ A: Calmodulin                                                                   SCOP domains
               CATH domains 1n0yA00 A:1-87 EF-hand                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....eehhhhhhhhhhh.....hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_ PROSITE (1)
                PROSITE (2) -------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1n0y A   1 AEQLTEEQIAEFKEAFALFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLSLMARKMKEQDSEEELIE  87
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:PROTEIN  Length:79
 aligned with CALM_PARTE | P07463 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:79
                                    79        89        99       109       119       129       139         
           CALM_PARTE    70 LSLMARKMKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLGEKLTDDEVDEMIREADIDGDGHINYEEFVRMMVS 148
               SCOP domains d1n0yb_ B: Calmodulin                                                           SCOP domains
               CATH domains 1n0yB00 B:69-147 EF-hand                                                        CATH domains
           Pfam domains (1) ----------EF_hand_5-1n0yB01 B:79-145                                         -- Pfam domains (1)
           Pfam domains (2) ----------EF_hand_5-1n0yB02 B:79-145                                         -- Pfam domains (2)
           Pfam domains (3) ----------EF_hand_5-1n0yB03 B:79-145                                         -- Pfam domains (3)
           Pfam domains (4) ----------EF_hand_5-1n0yB04 B:79-145                                         -- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhh........eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) EF_HAND_2 -EF_HAND_2  PDB: B:80-115            EF_HAND_2  PDB: B:116-147        PROSITE (1)
                PROSITE (2) ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1n0y B  69 LSLMARKMKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLGEKLTDDEVDEMIREADIDGDGHINYEEFVRMMVS 147
                                    78        88        98       108       118       128       138

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(

)

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: Calmodulin (152)

Ciliate (Paramecium tetraurelia) [TaxId: 5888] (4)

1a	d1n0ya_	A:
1b	d1n0yb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Paramecium tetraurelia. Organism_taxid: 5888. (1)

1a	1n0yA00	A:1-87
1b	1n0yB00	B:69-147

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_5 (126)

Paramecium tetraurelia (3)

1a	EF_hand_5-1n0yB01	B:79-145
1b	EF_hand_5-1n0yB02	B:79-145
1c	EF_hand_5-1n0yB03	B:79-145
1d	EF_hand_5-1n0yB04	B:79-145

Asymmetric Unit(hide GO term definitions)

Chain A,B (CALM_PARTE | P07463)

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.

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CAC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PB	[ 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 ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1n0y)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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
	1n0y
		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
	CALM_PARTE \| P07463
		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
	CALM_PARTE \| P07463
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CALM_PARTE \| P07463	:	1clm 1exr 1osa 2kxw 2m5e 5e1k 5e1n 5e1p

(no "Related Entries Specified in the PDB File" available for 1N0Y)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 9)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 4)

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