1WRZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CALMODULIN COMPLEXED WITH A PEPTIDE FROM A HUMAN DEATH-ASSOCIATED PROTEIN KINASE

Authors :   P. Kursula, J. Vahokoski, M. Wilmanns

Date :   29 Oct 04 (Deposition) - 21 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Calmodulin, Protein Kinase, Metal Binding Protein-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kursula, J. Vahokoski, M. Wilmanns
The Mode Of Binding Of Calmodulin To Death-Associated Protein Kinases
To Be Published
PubMed: search

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET8A
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - DEATH-ASSOCIATED PROTEIN KINASE 2
	Chains	:	B
	EC Number	:	2.7.1.37
	Engineered	:	YES
	Fragment	:	RESIDUES 302-320
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
	Synonym	:	DAP KINASE 2, DAP- KINASE RELATED PROTEIN 1, DRP-1
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31 , HOH A:5011	BINDING SITE FOR RESIDUE CA A 151
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67 , HOH A:5012	BINDING SITE FOR RESIDUE CA A 152
3	AC3	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104 , HOH A:5013	BINDING SITE FOR RESIDUE CA A 153
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140 , HOH A:5014	BINDING SITE FOR RESIDUE CA A 154

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

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

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_069222	N	54	I	CALM1_HUMAN	Disease (CPVT4)	267607276	A	N	53	I
2	UniProt	VAR_073275	F	90	L	CALM1_HUMAN	Disease (LQT14)	730882253	A	F	89	L
3	UniProt	VAR_078541	N	98	S	CALM1_HUMAN	Disease (CPVT4)	398124647	A	N	97	S
4	UniProt	VAR_078542	D	130	G	CALM1_HUMAN	Disease (LQT14)	730882252	A	D	129	G
5	UniProt	VAR_078263	E	141	G	CALM1_HUMAN	Disease (LQT14)	---	A	E	140	G
6	UniProt	VAR_073282	F	142	L	CALM1_HUMAN	Disease (LQT14)	11551462	A	F	141	L

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM1_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM1_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000261891	2	ENSE00002147850	chr15:64332466-64332369	98	DAPK2_HUMAN	1-31	31	0	-	-
1.3	ENST00000261891	3	ENSE00001770226	chr15:64275953-64275732	222	DAPK2_HUMAN	31-105	75	0	-	-
1.4	ENST00000261891	4	ENSE00001749190	chr15:64263760-64263622	139	DAPK2_HUMAN	105-151	47	0	-	-
1.5	ENST00000261891	5	ENSE00001698100	chr15:64231560-64231431	130	DAPK2_HUMAN	152-195	44	0	-	-
1.6	ENST00000261891	6	ENSE00001201925	chr15:64222654-64222606	49	DAPK2_HUMAN	195-211	17	0	-	-
1.7	ENST00000261891	7	ENSE00001281575	chr15:64221776-64221750	27	DAPK2_HUMAN	211-220	10	0	-	-
1.8	ENST00000261891	8	ENSE00001281565	chr15:64218292-64218140	153	DAPK2_HUMAN	220-271	52	0	-	-
1.9	ENST00000261891	9	ENSE00001281556	chr15:64217060-64217015	46	DAPK2_HUMAN	271-286	16	0	-	-
1.10	ENST00000261891	10	ENSE00001281547	chr15:64204396-64204307	90	DAPK2_HUMAN	287-316	30	1	B:302-306	5
1.11a	ENST00000261891	11a	ENSE00001281540	chr15:64204190-64204107	84	DAPK2_HUMAN	317-344	28	1	B:307-320	14
1.12b	ENST00000261891	12b	ENSE00001281614	chr15:64200799-64199235	1565	DAPK2_HUMAN	345-370	26	0	-	-

2.1	ENST00000356978	1	ENSE00001405603	chr14:90863373-90863577	205	CALM1_HUMAN	1-1	1	0	-	-
2.3	ENST00000356978	3	ENSE00001004657	chr14:90866409-90866439	31	CALM1_HUMAN	2-12	11	1	A:2-11	10
2.4	ENST00000356978	4	ENSE00001684420	chr14:90867603-90867746	144	CALM1_HUMAN	12-60	49	1	A:11-59	49
2.5	ENST00000356978	5	ENSE00001656881	chr14:90870206-90870312	107	CALM1_HUMAN	60-95	36	1	A:59-94	36
2.6	ENST00000356978	6	ENSE00001746010	chr14:90870723-90870858	136	CALM1_HUMAN	96-141	46	1	A:95-140	46
2.7b	ENST00000356978	7b	ENSE00001373724	chr14:90871033-90874610	3578	CALM1_HUMAN	141-149	9	1	A:140-148	9

Asymmetric/Biological 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:147
 aligned with CALM1_HUMAN | P0DP23 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       
          CALM1_HUMAN     3 DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains d1wrza_ A: Calmodulin                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------I-----------------------------------L-------S-------------------------------G----------GL------- SAPs(SNPs)
                PROSITE (1) -----EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (1)
                PROSITE (2) ------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (2)
           Transcript 2 (1) Exon 2.3  -----------------------------------------------Exon 2.5  PDB: A:59-94              Exon 2.6  PDB: A:95-140 UniProt: 96-141       -------- Transcript 2 (1)
           Transcript 2 (2) ---------Exon 2.4  PDB: A:11-59 UniProt: 12-60            --------------------------------------------------------------------------------Exon 2.7b Transcript 2 (2)
                 1wrz A   2 DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:19
 aligned with DAPK2_HUMAN | Q9UIK4 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:19
                                   321         
          DAPK2_HUMAN   312 RRRWKLSFSIVSLCNHLTR 330
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
               Transcript 1 1.10 Exon 1.11a     Transcript 1
                 1wrz B 302 RRRWKLSFSIVSLCNHLTR 320
                                   311

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/Biological 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)

Human (Homo sapiens) [TaxId: 9606] (74)

d1wrza_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CALM1_HUMAN | P0DP23)

Chain B (DAPK2_HUMAN | Q9UIK4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0043276	anoikis	Apoptosis triggered by inadequate or inappropriate adherence to substrate e.g. after disruption of the interactions between normal epithelial cells and the extracellular matrix.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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:1990266	neutrophil migration	The movement of an neutrophil within or between different tissues and organs of the body.
	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:2000424	positive regulation of eosinophil chemotaxis	Any process that activates or increases the frequency, rate or extent of eosinophil chemotaxis.
	GO:0090023	positive regulation of neutrophil chemotaxis	Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0010506	regulation of autophagy	Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:2001242	regulation of intrinsic apoptotic signaling pathway	Any process that modulates the frequency, rate or extent of intrinsic apoptotic signaling pathway.
cellular component
	GO:0034423	autophagosome lumen	The volume enclosed within the autophagosome double-membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.

Asymmetric/Biological 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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	1wrz
		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
	CALM1_HUMAN \| P0DP23
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	DAPK2_HUMAN \| Q9UIK4
		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)
	2.7.1.37
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	614916
		Disease Information	:	OMIM
	616247
		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
	CALM1_HUMAN \| P0DP23
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	DAPK2_HUMAN \| Q9UIK4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (2, 8)

Exons (7, 7)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (103, 105)

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