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(-) Description

Title :  CA2+-BOUND STRUCTURE OF MULTIDOMAIN EF-HAND PROTEIN, CBP40, FROM TRUE SLIME MOLD
 
Authors :  W. Iwasaki, H. Sasaki, A. Nakamura, K. Kohama, M. Tanokura
Date :  25 Apr 01  (Deposition) - 11 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Fourty Kda Calcium Binding Protein, Cbp40, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Iwasaki, H. Sasaki, A. Nakamura, K. Kohama, M. Tanokura
Metal-Free And Ca(2+)-Bound Structures Of A Multidomain Ef-Hand Protein, Cbp40, From The Lower Eukaryote Physarum Polycephalum
Structure V. 11 75 2003
PubMed-ID: 12517342  |  Reference-DOI: 10.1016/S0969-2126(02)00932-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMODIAL SPECIFIC LAV1-2 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 33-355
    Organism Scientific: PHYSARUM POLYCEPHALUM
    Organism Taxid: 5791

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:230 , ASN A:232 , ASN A:234 , THR A:236 , GLU A:241BINDING SITE FOR RESIDUE CA A 356
2AC2SOFTWAREASP A:265 , ASP A:267 , SER A:269 , ASP A:271 , GLU A:276BINDING SITE FOR RESIDUE CA A 357
3AC3SOFTWAREASP A:295 , ASP A:297 , SER A:299 , GLN A:301 , GLU A:306BINDING SITE FOR RESIDUE CA A 358
4AC4SOFTWAREASP A:332 , ASP A:334 , SER A:336 , SER A:338 , GLU A:343BINDING SITE FOR RESIDUE CA A 359

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IJ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IJ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IJ6)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.LAV1_PHYPO151-186
217-252
282-317
319-354		  4A:151-186
A:217-252
A:282-317
A:319-353
2EF_HAND_1PS00018 EF-hand calcium-binding domain.LAV1_PHYPO230-242
265-277
295-307
332-344		  4A:230-242
A:265-277
A:295-307
A:332-344

(-) Exons   (0, 0)

(no "Exon" information available for 1IJ6)

(-) 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:305
 aligned with LAV1_PHYPO | P14725 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:321
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352 
           LAV1_PHYPO    33 EIFSQELTQREANVKKVHENLEELQKKLDHTSFAHKEDRDRLEAQIAQKEQEQKAKLAEYDQKVQNEFDARERAEREREAARGDAAAEKQRLASLLKDLEDDASGYNRLRPSKPMLSEEDTNILRQLFLSSAVSGSGKFSFQDLKQVLAKYADTIPEGPLKKLFVMVENDTKGRMSYITLVAVANDLAALVADFRKIDTNSNGTLSRKEFREHFVRLGFDKKSVQDALFRYADEDESDDVGFSEYVHLGLCLLVLRILYAFADFDKSGQLSKEEVQKVLEDAHIPESARKKFEHQFSVVDVDDSKSLSYQEFVMLVLLMFH 353
               SCOP domains d1ij6a_ A: Cbp40 (plasmodial specif    ic CaII-binding protein LAV1-2)                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1ij6A01 A:33-112  [code=1.20.58.90,     no name defined]                        --------------------            ------------------------------------------------------------------------------1ij6A03 A:223-353 EF-hand                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh......----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..------------....hhhhhhhhhhhhh..........hhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhh.hhhhhh.....eehhhhhhhhhhhhh..hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhhh..hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------EF_HAND_2  PDB: A:151-186           ------------------------------EF_HAND_2  PDB: A:217-252           ------------EF_HAND_1    ----EF_HAND_2  PDB: A:282-317           -EF_HAND_2  PDB: A:319-353           PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_1    ----------------------------------------------------EF_HAND_1    ------------------------EF_HAND_1    --------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ij6 A  33 EIFSQELTQREANVKKVHENLEELQKKLDHTSFAH----DRLEAQIAQKEQEQKAKLAEYDQKVQNEFDARERAEREREAARGDAAAEKQRLASLLKDLE------------KPMLSEEDTNILRQLFLSSAVSGSGKFSFQDLKQVLAKYADTIPEGPLKKLFVMVENDTKGRMSYITLVAVANDLAALVADFRKIDTNSNGTLSRKEFREHFVRLGFDKKSVQDALFRYADEDESDDVGFSEYVHLGLCLLVLRILYAFADFDKSGQLSKEEVQKVLEDAHIPESARKKFEHQFSVVDVDDSKSLSYQEFVMLVLLMFH 353
                                    42        52        62    |   72        82        92       102       112       122       132         -  |    152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352 
                                                             67   72                                                         132          145
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IJ6)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LAV1_PHYPO | P14725)
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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  1ij6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LAV1_PHYPO | P14725: 1ij5

(-) Related Entries Specified in the PDB File

1ij5 1IJ5 CONTAINS THE SAME PROTEIN (METAL-FREE).