1Y6W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   TRAPPED INTERMEDIATE OF CALMODULIN

Authors :   Z. Grabarek

Date :   07 Dec 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

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

Reference :   Z. Grabarek
Structure Of A Trapped Intermediate Of Calmodulin: Calcium Regulation Of Ef-Hand Proteins From A New Perspective.
J. Mol. Biol. V. 346 1351 2005
PubMed-ID: 15713486 | Reference-DOI: 10.1016/J.JMB.2005.01.004
(for further references see the PDB file header)

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PAED4
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	CALM1, CALM2, CALM3
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CAM

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 15)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
4	TBU	1	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , HOH A:602 , HOH A:606	BINDING SITE FOR RESIDUE CA A 149
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , MPD A:400	BINDING SITE FOR RESIDUE CA A 150
3	AC3	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104 , HOH A:611	BINDING SITE FOR RESIDUE CA A 151
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140 , HOH A:604	BINDING SITE FOR RESIDUE CA A 152
5	AC5	SOFTWARE	THR A:26 , ARG A:37 , SER A:38 , ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , ASN A:64 , GLU A:67 , CA A:150	BINDING SITE FOR RESIDUE MPD A 400
6	AC6	SOFTWARE	LEU A:105 , MSE A:144	BINDING SITE FOR RESIDUE TBU A 500

Asymmetric/Biological Unit

No.	Residues
1	A:41	-	A:75

(no "Cis Peptide Bond" information available for 1Y6W)

Asymmetric/Biological Unit (15, 15)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_069222	N	54	I	CALM1_HUMAN	Disease (CPVT4)	267607276	A	N	53	I
02	UniProt	VAR_073275	F	90	L	CALM1_HUMAN	Disease (LQT14)	730882253	A	F	89	L
03	UniProt	VAR_073276	D	96	V	CALM2_HUMAN	Disease (LQT15)	730882254	A	D	95	V
04	UniProt	VAR_073277	N	98	I	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	I
05	UniProt	VAR_078541	N	98	S	CALM1_HUMAN	Disease (CPVT4)	398124647	A	N	97	S
06	UniProt	VAR_078543	N	98	S	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	S
07	UniProt	VAR_078261	A	103	V	CALM3_HUMAN	Disease	---	A	A	102	V
08	UniProt	VAR_078542	D	130	G	CALM1_HUMAN	Disease (LQT14)	730882252	A	D	129	G
09	UniProt	VAR_078544	D	130	G	CALM2_HUMAN	Disease (LQT15)	730882252	A	D	129	G
10	UniProt	VAR_078262	D	130	V	CALM2_HUMAN	Disease (LQT15)	---	A	D	129	V
11	UniProt	VAR_073279	D	132	E	CALM2_HUMAN	Disease (LQT15)	398124648	A	D	131	E
12	UniProt	VAR_073280	D	134	H	CALM2_HUMAN	Disease (LQT15)	398124650	A	D	133	H
13	UniProt	VAR_073281	Q	136	P	CALM2_HUMAN	Disease (LQT15)	398124649	A	Q	135	P
14	UniProt	VAR_078263	E	141	G	CALM1_HUMAN	Disease (LQT14)	---	A	E	140	G
15	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:116-147
				CALM2_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-147
				CALM3_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-147
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
				CALM2_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM3_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

(no "Exon" information available for 1Y6W)

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:145
 aligned with CALM1_HUMAN | P0DP23 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     
          CALM1_HUMAN     4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 148
               SCOP domains d1y6wa_ A: Calmodulin                                                                                                                             SCOP domains
               CATH domains 1y6wA01 A:3-78 EF-hand                                                      1y6wA02 A:79-147 EF-hand                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....eeehhhhhhhhhhh....hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------S-------------------------------G------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------S-------------------------------V------------------ SAPs(SNPs) (3)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----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:116-147        PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (5)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6w A   3 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVmRSLGCNPTEAELQDmINEVDADGNGTINFPEFLTmmARCmKDTDSEEEIREAFRVFDKDGNGYISAAELRHVmTNLGEKLTDEEVDEmIREADIDGDGQVNYEEFVQmmTA 147
                                    12        22        32   |    42        52        62        72   |    82        92       102      |112       122 |     132       142 ||  
                                                            36-MSE         51-MSE              71-MSE|                              109-MSE        124-MSE             144-MSE
                                                                                                72-MSE                                                                  145-MSE
                                                                                                    76-MSE

Chain A from PDB  Type:PROTEIN  Length:145
 aligned with CALM2_HUMAN | P0DP24 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     
          CALM2_HUMAN     4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 148
               SCOP domains d1y6wa_ A: Calmodulin                                                                                                                             SCOP domains
               CATH domains 1y6wA01 A:3-78 EF-hand                                                      1y6wA02 A:79-147 EF-hand                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....eeehhhhhhhhhhh....hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------S-------------------------------G------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------S-------------------------------V------------------ SAPs(SNPs) (3)
                PROSITE (2) ----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:116-147        PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6w A   3 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVmRSLGCNPTEAELQDmINEVDADGNGTINFPEFLTmmARCmKDTDSEEEIREAFRVFDKDGNGYISAAELRHVmTNLGEKLTDEEVDEmIREADIDGDGQVNYEEFVQmmTA 147
                                    12        22        32   |    42        52        62        72   |    82        92       102      |112       122 |     132       142 ||  
                                                            36-MSE         51-MSE              71-MSE|                              109-MSE        124-MSE             144-MSE
                                                                                                72-MSE                                                                  145-MSE
                                                                                                    76-MSE

Chain A from PDB  Type:PROTEIN  Length:145
 aligned with CALM3_HUMAN | P0DP25 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     
          CALM3_HUMAN     4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 148
               SCOP domains d1y6wa_ A: Calmodulin                                                                                                                             SCOP domains
               CATH domains 1y6wA01 A:3-78 EF-hand                                                      1y6wA02 A:79-147 EF-hand                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....eeehhhhhhhhhhh....hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------S-------------------------------G------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------S-------------------------------V------------------ SAPs(SNPs) (3)
                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:116-147        PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (6)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6w A   3 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVmRSLGCNPTEAELQDmINEVDADGNGTINFPEFLTmmARCmKDTDSEEEIREAFRVFDKDGNGYISAAELRHVmTNLGEKLTDEEVDEmIREADIDGDGQVNYEEFVQmmTA 147
                                    12        22        32   |    42        52        62        72   |    82        92       102      |112       122 |     132       142 ||  
                                                            36-MSE         51-MSE              71-MSE|                              109-MSE        124-MSE             144-MSE
                                                                                                72-MSE                                                                  145-MSE
                                                                                                    76-MSE

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)

d1y6wa_

Asymmetric/Biological 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)

Human (Homo sapiens) (106)

1a	1y6wA01	A:3-78
1b	1y6wA02	A:79-147

(no "Pfam Domain" information available for 1Y6W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CALM1_HUMAN | P0DP23)

Chain A (CALM3_HUMAN | P0DP25)

Chain A (CALM2_HUMAN | P0DP24)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y6w)

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	1y6w
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (6, 6)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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