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(-) Description

Title :  FRAC WITH GLCNAC(6S) BOUND
 
Authors :  J. M. M. Caaveiro, K. Tsumoto
Date :  11 Sep 16  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Actinoporin, Pore-Forming Toxin, Carbohydrate-Protein Interaction, Lipid-Protein Interaction, Toxin, Cytolysin, Nanopore (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tanaka, J. M. M. Caaveiro, K. Morante, K. Tsumoto
Hemolytic Actinoporins Interact With Carbohydrates Using Their Lipid-Binding Module
Philos. Trans. R. Soc. Lond. B 2017 Biol. Sci.
PubMed: search  |  Reference-DOI: 10.1098/RSTB.2016.0216

(-) Compounds

Molecule 1 - DELTA-ACTITOXIN-AFR1A
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: STRAWBERRY ANEMONE
    Organism Scientific: ACTINIA FRAGACEA
    Organism Taxid: 396334
    Synonym: DELTA-AITX-AFR1A,CYTOLYSIN FRAGACEATOXIN C,FRAC

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1CL13Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NGY2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3NGY-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NGY1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NGY-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3NGY1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:113 , SER A:114 , TRP A:116 , HOH A:314 , HOH A:330binding site for residue CL A 201
02AC2SOFTWAREARG B:53 , GLN B:130 , TYR B:133 , GLU B:134 , TYR B:138 , HOH B:302 , HOH B:318 , HOH B:430binding site for residue NGY B 201
03AC3SOFTWARETYR B:113 , SER B:114 , TRP B:116 , HOH B:307 , HOH B:346binding site for residue CL B 202
04AC4SOFTWARELEU B:61 , HOH B:326 , HOH B:438binding site for residue CL B 203
05AC5SOFTWAREPHE B:16 , ASP B:17 , LYS C:64 , HOH C:466binding site for residue CL B 204
06AC6SOFTWAREARG A:144 , LYS B:123binding site for residue CL B 205
07AC7SOFTWAREARG B:161 , HIS B:175 , HOH B:395 , HOH C:363binding site for residue CL B 206
08AC8SOFTWAREGLY B:85 , TYR B:108binding site for residue CL B 207
09AC9SOFTWAREGLY B:15 , PHE B:16 , GLU B:173 , HOH B:306 , HOH B:356 , HOH B:357 , HOH B:359 , HOH B:371 , MET C:94 , GLY C:97 , GLN C:125binding site for residue GOL B 208
10AD1SOFTWARETYR C:113 , SER C:114 , TRP C:116 , HOH C:308 , HOH C:329binding site for residue CL C 201
11AD2SOFTWAREARG C:120 , LYS C:123 , HOH C:319binding site for residue CL C 202
12AD3SOFTWARESER C:54 , GLY C:85 , TYR C:108binding site for residue CL C 203
13AD4SOFTWARETRP B:149 , ARG B:161 , HOH B:306 , ASP C:96 , GLY C:97 , ASN C:98 , LYS C:123binding site for residue GOL C 204
14AD5SOFTWAREARG D:53 , GLN D:130 , TYR D:133 , GLU D:134 , TYR D:138 , HOH D:317 , HOH D:337 , HOH D:348 , HOH D:351 , HOH D:420binding site for residue NGY D 201
15AD6SOFTWARELEU D:61 , HOH D:428binding site for residue CL D 202
16AD7SOFTWARETYR D:113 , SER D:114 , TRP D:116 , HOH D:331 , HOH D:387binding site for residue CL D 203
17AD8SOFTWARESER D:54 , GLY D:85 , TYR D:108binding site for residue CL D 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GWF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GWF)

(-) 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:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gwf A   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gwf B   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       


Chain C from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee....eeeeeeee.........eeeeeee......hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gwf C   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       


Chain D from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeeeeee.........ee...eeeeeeee.........eeeeeeeee...eeeeeeeee.........eeeeeeee.....hhhhhhhhhhh...ee...eeeeeeee..eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gwf D   3 DVAGAVIDGAGLGFDVLKTVLEALGNVKRKIAVGIDNESGKTWTAMNTYFRSGTSDIVLPHKVAHGKALLYNGQKNRGPVATGVVGVIAYSMSDGNTLAVLFSVPYDYNWYSNWWNVRVYKGQKRADQRMYEELYYHRSPFRGDNGWHSRGLGYGLKSRGFMNSSGHAILEIHVTKA 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        ACTPC_ACTFR | B9W5G6: 3lim 3vwi 3w9p 3zwg 3zwj 4tsl 4tsn 4tso 4tsp 4tsq 4tsy 4wdc 5bpg

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