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(-) Description

Title :  STRUCTURAL ANALYSIS OF A HOMOLOG OF PROGRAMMED CELL DEATH 6 PROTEIN FROM LEISHMANIA MAJOR FRIEDLIN
 
Authors :  M. A. Robien, W. G. J. Hol, Structural Genomics Of Pathogenic Proto Consortium (Sgpp)
Date :  19 Nov 04  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Sgpp, Structural Genomics, Psi, Protein Structure Initiative, Structural Genomics Of Pathogenic Protozoa Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Robien, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp
Structural Analysis Of A Homolog Of Programmed Cell Death 6 Protein From Leishmania Major Friedlin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LEISHMANIA MAJOR HOMOLOG OF PROGRAMMED CELL DEATH 6 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 53-234
    Gene: LMJF13.1460
    Mutation: YES
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 347515
    Strain: FRIEDLIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:37 , ASP A:39 , SER A:41 , ALA A:43 , GLU A:48 , HOH A:508BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREASP A:73 , ASN A:75 , SER A:77 , GLU A:79 , GLU A:84 , HOH A:554BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWARESER A:61 , LEU A:62 , ALA A:63BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREARG A:34 , SER A:112 , ARG A:116 , GLN A:132 , ARG B:34BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWAREASP B:37 , ASP B:39 , SER B:41 , ALA B:43 , GLU B:48 , HOH B:558BINDING SITE FOR RESIDUE CA B 211
6AC6SOFTWAREASP B:73 , ASN B:75 , SER B:77 , GLU B:79 , GLU B:84 , HOH B:597BINDING SITE FOR RESIDUE CA B 212
7AC7SOFTWARESER B:61 , LEU B:62 , ALA B:63BINDING SITE FOR RESIDUE SO4 B 213

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y1X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y1X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y1X)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y1X)

(-) Sequences/Alignments

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:182
 aligned with Q4QG08_LEIMA | Q4QG08 from UniProtKB/TrEMBL  Length:234

    Alignment length:182
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
         Q4QG08_LEIMA    53 PTSTGVYAPSARHMNDNQELMEWFRAVDTDGSGAISVPELNAALSSAGVPFSLATTEKLLHMYDKNHSGEITFDEFKDLHHFILSMREGFRKRDSSGDGRLDSNEVRAALLSSGYQVSEQTFQALMRKFDRQRRGSLGFDDYVELSIFVCRVRNVFAFYDRERTGQVTFTFDTFIGGSVSIL 234
               SCOP domains d1y1xa_ A: Programmed cell death 6 protein-like protein                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhh.......hhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y1x A  10 PTSTGVYAPSARHMNDNQELMEWFRAVDTDGSGAISVPELNAALSSAGVPFSLATTEKLLHMYDKNHSGEITFDEFKDLHHFILSMREGFRKRDSSGDGRLDSNEVRAALLSSGYQVSEQTFQALMRKFDRQRRGSLGFDDYVELSIFVCRVRNVFAFYDRERTGQVTFTFDTFIGGSVSIL 191
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189  


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with Q4QG08_LEIMA | Q4QG08 from UniProtKB/TrEMBL  Length:234

    Alignment length:181
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
         Q4QG08_LEIMA    54 TSTGVYAPSARHMNDNQELMEWFRAVDTDGSGAISVPELNAALSSAGVPFSLATTEKLLHMYDKNHSGEITFDEFKDLHHFILSMREGFRKRDSSGDGRLDSNEVRAALLSSGYQVSEQTFQALMRKFDRQRRGSLGFDDYVELSIFVCRVRNVFAFYDRERTGQVTFTFDTFIGGSVSIL 234
               SCOP domains d1y1xb_ B       : Programmed cell death 6 protein-like protein                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------EF_hand_4-1y1xB01 B:66-93   -------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------EF_hand_4-1y1xB02 B:66-93   -------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------EF_hand_5-1y1xB03 B:92-155                                      ------------------------------------ Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------EF_hand_5-1y1xB04 B:92-155                                      ------------------------------------ Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------EF_hand_5-1y1xB05 B:92-155                                      ------------------------------------ Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------EF_hand_5-1y1xB06 B:92-155                                      ------------------------------------ Pfam domains (6)
         Sec.struct. author .........-------.hhhhhhhhhh.......hhhhhhhhhh......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y1x B  11 TSTGVYAPS-------QELMEWFRAVDTDGSGAISVPELNAALSSAGVPFSLATTEKLLHMYDKNHSGEITFDEFKDLHHFILSMREGFRKRDSSGDGRLDSNEVRAALLSSGYQVSEQTFQALMRKFDRQRRGSLGFDDYVELSIFVCRVRNVFAFYDRERTGQVTFTFDTFIGGSVSIL 191
                                    |-      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
                                   19      27
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y1X)

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q4QG08_LEIMA | Q4QG08)
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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