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(-) Description

Title :  CRYSTAL STRUCTURE OF S202G MUTANT OF HUMAN SYT-5 C2A DOMAIN
 
Authors :  X. Qiu, J. Ge, X. Yan, Y. Gao, M. Teng, L. Niu
Date :  02 Nov 16  (Deposition) - 30 Nov 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metal Binding Protein, Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Qiu, J. Ge, Y. Gao, M. Teng, L. Niu
Structural Analysis Of Ca(2+)-Binding Pocket Of Synaptotagmin 5 C2A Domain
Int. J. Biol. Macromol. V. 95 946 2017
PubMed-ID: 27793683  |  Reference-DOI: 10.1016/J.IJBIOMAC.2016.10.083

(-) Compounds

Molecule 1 - SYNAPTOTAGMIN-5
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP28
    Expression System Taxid562
    FragmentUNP RESIDUES 102-242
    GeneSYT5
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSYNAPTOTAGMIN V,SYTV

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:139 , ASP A:145 , ASP A:197 , PHE A:198 , ASP A:199 , CA A:302 , HOH A:404binding site for residue CA A 301
2AC2SOFTWARELEU A:138 , ASP A:139 , ASP A:197 , ASP A:199 , ASP A:205 , ASP A:218 , CA A:301binding site for residue CA A 302
3AC3SOFTWAREASP A:199 , ARG A:203 , ASP A:205 , ASP A:218 , HOH A:416 , HOH A:417binding site for residue CA A 303
4AC4SOFTWAREASP B:139 , ASP B:145 , ASP B:197 , PHE B:198 , ASP B:199binding site for residue CA B 301
5AC5SOFTWARELEU B:138 , ASP B:139 , ASP B:197 , ASP B:199 , ASP B:205 , HOH B:405binding site for residue CA B 302
6AC6SOFTWAREASP B:199 , ARG B:203 , ASP B:205 , HOH B:403 , HOH B:405binding site for residue CA B 303
7AC7SOFTWAREGLU A:228 , GLU B:228binding site for residue CL B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H4Z)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:153 -Pro A:154
2Leu B:153 -Pro B:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5H4Z)

(-) 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:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee....eeeeeeeeee............eeeeeeee.eeeeeee..........eeeeeeeee.........eeeeeeee.......eeeeeeeee.hhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h4z A 105 DKHELGQLQYSLDYDFQSGQLLVGILQAMGLAALDLGGSSDPYVRVYLLPDKRRRYETKVHRQTLNPHFGETFAFKVPYVELGGRVLVMAVYDFDRFGRNDAIGEVRVPMSSVDLGRPVQAWRELQAAP 233
                                   114       124       134       144       154       164       174       184       194       204       214       224         

Chain B from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee............eeeeeeee.eeeeeee..........eeeeeeeee..hhhhh..eeeeeeee.......eeeeeeeee.hhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h4z B 106 KHELGQLQYSLDYDFQSGQLLVGILQAMGLAALDLGGSSDPYVRVYLLPDKRRRYETKVHRQTLNPHFGETFAFKVPYVELGGRVLVMAVYDFDRFGRNDAIGEVRVPMSSVDLGRPVQAWRELQAAP 233
                                   115       125       135       145       155       165       175       185       195       205       215       225        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5H4Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H4Z)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYT5_HUMAN | O004455h4y

(-) Related Entries Specified in the PDB File

5h4y