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(-) Description

Title :  STRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM NEREIS DIVERSICOLOR REFINED AT 2.0 ANGSTROMS RESOLUTION
 
Authors :  W. J. Cook, S. Vijay-Kumar
Date :  22 Aug 91  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Vijay-Kumar, W. J. Cook
Structure Of A Sarcoplasmic Calcium-Binding Protein From Nereis Diversicolor Refined At 2. 0 A Resolution.
J. Mol. Biol. V. 224 413 1992
PubMed-ID: 1560459  |  Reference-DOI: 10.1016/0022-2836(92)91004-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SARCOPLASMIC CALCIUM-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Organism Scientific: NEANTHES DIVERSICOLOR
    Organism Taxid: 6352

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:16 , ASP A:18 , ASP A:20 , ALA A:22 , ASP A:27 , HOH A:193BINDING SITE FOR RESIDUE CA A 190
02AC2SOFTWAREASP A:104 , ASN A:106 , ASP A:108 , ASN A:110 , GLU A:115 , HOH A:199BINDING SITE FOR RESIDUE CA A 191
03AC3SOFTWAREASP A:138 , ASN A:140 , ASP A:142 , LEU A:144 , GLU A:149 , HOH A:205BINDING SITE FOR RESIDUE CA A 192
04AC4SOFTWAREASP B:16 , ASP B:18 , ASP B:20 , ALA B:22 , ASP B:27 , HOH B:196BINDING SITE FOR RESIDUE CA B 193
05AC5SOFTWAREASP B:104 , ASN B:106 , ASP B:108 , ASN B:110 , GLU B:115BINDING SITE FOR RESIDUE CA B 194
06AC6SOFTWAREASP B:138 , ASN B:140 , ASP B:142 , LEU B:144 , GLU B:149 , HOH B:207BINDING SITE FOR RESIDUE CA B 195
07EF1UNKNOWNASP A:16 , PHE A:17 , ASP A:18 , LYS A:19 , ASP A:20 , GLY A:21 , ALA A:22 , ILE A:23 , THR A:24 , ARG A:25 , MET A:26 , ASP A:27NULL
08EF2UNKNOWNASP A:104 , THR A:105 , ASN A:106 , GLU A:107 , ASP A:108 , ASN A:109 , ASN A:110 , ILE A:111 , SER A:112 , ARG A:113 , ASP A:114 , GLU A:115NULL
09EF3UNKNOWNASP A:138 , THR A:139 , ASN A:140 , ASN A:141 , ASP A:142 , GLY A:143 , LEU A:144 , LEU A:145 , SER A:146 , LEU A:147 , GLU A:148 , GLU A:149NULL
10EF4UNKNOWNASP B:16 , PHE B:17 , ASP B:18 , LYS B:19 , ASP B:20 , GLY B:21 , ALA B:22 , ILE B:23 , THR B:24 , ARG B:25 , MET B:26 , ASP B:27NULL
11EF5UNKNOWNASP B:104 , THR B:105 , ASN B:106 , GLU B:107 , ASP B:108 , ASN B:109 , ASN B:110 , ILE B:111 , SER B:112 , ARG B:113 , ASP B:114 , GLU B:115NULL
12EF6UNKNOWNASP B:138 , THR B:139 , ASN B:140 , ASN B:141 , ASP B:142 , GLY B:143 , LEU B:144 , LEU B:145 , SER B:146 , LEU B:147 , GLU B:148 , GLU B:149NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2SCP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2SCP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2SCP)

(-) PROSITE Motifs  (2, 12)

Asymmetric/Biological Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.SCP_HEDDI3-38
 
99-126
 
134-160
 		  6A:3-38
B:3-38
A:99-126
B:99-126
A:134-160
B:134-160
2EF_HAND_1PS00018 EF-hand calcium-binding domain.SCP_HEDDI16-28
 
104-116
 
138-150
 		  6A:16-28
B:16-28
A:104-116
B:104-116
A:138-150
B:138-150

(-) Exons   (0, 0)

(no "Exon" information available for 2SCP)

(-) Sequences/Alignments

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:174
 aligned with SCP_HEDDI | P04571 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
            SCP_HEDDI     1 SDLWVQKMKTYFNRIDFDKDGAITRMDFESMAERFAKESEMKAEHAKVLMDSLTGVWDNFLTAVAGGKGIDETTFINSMKEMVKNPEAKSVVEGPLPLFFRAVDTNEDNNISRDEYGIFFGMLGLDKTMAPASFDAIDTNNDGLLSLEEFVIAGSDFFMNDGDSTNKVFWGPLV 174
               SCOP domains d2scpa_ A: Sarcoplasmic calcium-binding protein                                                                                                                                SCOP domains
               CATH domains 2scpA00 A:1-174 EF-hand                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eeehhhhhhhhhh....hhhhhhhhhhh......eeehhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --EF_HAND_2  PDB: A:3-38 UniProt: 3-38------------------------------------------------------------EF_HAND_2  PDB: A:99-126    -------EF_HAND_2  PDB: A:134-160  -------------- PROSITE (1)
                PROSITE (2) ---------------EF_HAND_1    ---------------------------------------------------------------------------EF_HAND_1    ---------------------EF_HAND_1    ------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2scp A   1 SDLWVQKMKTYFNRIDFDKDGAITRMDFESMAERFAKESEMKAEHAKVLMDSLTGVWDNFLTAVAGGKGIDETTFINSMKEMVKNPEAKSVVEGPLPLFFRAVDTNEDNNISRDEYGIFFGMLGLDKTMAPASFDAIDTNNDGLLSLEEFVIAGSDFFMNDGDSTNKVFWGPLV 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with SCP_HEDDI | P04571 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
            SCP_HEDDI     1 SDLWVQKMKTYFNRIDFDKDGAITRMDFESMAERFAKESEMKAEHAKVLMDSLTGVWDNFLTAVAGGKGIDETTFINSMKEMVKNPEAKSVVEGPLPLFFRAVDTNEDNNISRDEYGIFFGMLGLDKTMAPASFDAIDTNNDGLLSLEEFVIAGSDFFMNDGDSTNKVFWGPLV 174
               SCOP domains d2scpb_ B: Sarcoplasmic calcium-binding protein                                                                                                                                SCOP domains
               CATH domains 2scpB00 B:1-174 EF-hand                                                                                                                                                        CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------EF_hand_3-2scpB01     --------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------EF_hand_3-2scpB02     --------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------EF_hand_3-2scpB03     --------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------EF_hand_3-2scpB04     --------------------- Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------------------------------------------------------EF_hand_3-2scpB05     --------------------- Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------------------------------------------------------------------------------EF_hand_3-2scpB06     --------------------- Pfam domains (6)
         Sec.struct. author hhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eeehhhhhhhhhh....hhhhhhhhhhh......eeehhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --EF_HAND_2  PDB: B:3-38 UniProt: 3-38------------------------------------------------------------EF_HAND_2  PDB: B:99-126    -------EF_HAND_2  PDB: B:134-160  -------------- PROSITE (1)
                PROSITE (2) ---------------EF_HAND_1    ---------------------------------------------------------------------------EF_HAND_1    ---------------------EF_HAND_1    ------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2scp B   1 SDLWVQKMKTYFNRIDFDKDGAITRMDFESMAERFAKESEMKAEHAKVLMDSLTGVWDNFLTAVAGGKGIDETTFINSMKEMVKNPEAKSVVEGPLPLFFRAVDTNEDNNISRDEYGIFFGMLGLDKTMAPASFDAIDTNNDGLLSLEEFVIAGSDFFMNDGDSTNKVFWGPLV 174
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SCP_HEDDI | P04571)
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.

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        SCP_HEDDI | P04571: 1q80

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