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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VIBRIO VULNIFICUS HEMOLYSIN/CYTOLYSIN BETA-TREFOIL LECTIN WITH N-ACETYL-D-LACTOSAMINE BOUND
 
Authors :  K. Kaus, R. Olson
Date :  02 Feb 14  (Deposition) - 28 May 14  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B,C,D,E,F,G  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  D  (1x)
Biol. Unit 6:  E  (1x)
Biol. Unit 7:  F  (1x)
Biol. Unit 8:  G  (1x)
Keywords :  Lectin, Pore-Forming Toxin, Beta-Trefoil, R-Type Lectin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kaus, J. W. Lary, J. L. Cole, R. Olson
Glycan Specificity Of The Vibrio Vulnificus Hemolysin Lecti Outlines Evolutionary History Of Membrane Targeting By A Toxin Family.
J. Mol. Biol. V. 426 2800 2014
PubMed-ID: 24862282  |  Reference-DOI: 10.1016/J.JMB.2014.05.021

(-) Compounds

Molecule 1 - CYTOLYSIN
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNGFP-BC
    Expression System Strain: NEB SHUFFLE T7 EXPRESS
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 338-471
    Gene: VV2_0404,VVHA
    Organism Scientific: VIBRIO VULNIFICUS
    Organism Taxid: 216895
    Strain: CMCP6

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): ABCDEFG
Biological Unit 2 (1x): A      
Biological Unit 3 (1x):  B     
Biological Unit 4 (1x):   C    
Biological Unit 5 (1x):    D   
Biological Unit 6 (1x):     E  
Biological Unit 7 (1x):      F 
Biological Unit 8 (1x):       G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1GAL6Ligand/IonBETA-D-GALACTOSE
2GOL5Ligand/IonGLYCEROL
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1GAL6Ligand/IonBETA-D-GALACTOSE
2GOL5Ligand/IonGLYCEROL
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GAL-1Ligand/IonBETA-D-GALACTOSE
2GOL1Ligand/IonGLYCEROL
3NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL-1Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL1Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 5 (3, 3)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL1Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 6 (3, 3)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL1Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 7 (3, 3)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL1Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 8 (1, 1)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL-1Ligand/IonGLYCEROL
3NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:353 , VAL A:354 , TYR A:355 , LYS A:361 , TRP A:371 , HIS A:374 , ASN A:378binding site for residue GOL A 501
02AC2SOFTWARETRP C:422 , GLY C:424 , PRO C:464 , HOH C:616binding site for residue GOL C 503
03AC3SOFTWARETRP D:422 , GLY D:424 , PRO D:464 , HOH D:652binding site for residue GOL D 503
04AC4SOFTWARETRP E:422 , GLY E:424 , PRO E:464 , HOH E:650binding site for residue GOL E 503
05AC5SOFTWARETRP F:422 , GLY F:424 , HOH F:663binding site for residue GOL F 503
06AC6SOFTWAREASP G:353 , VAL G:354 , TRP G:371 , HIS G:374 , ASN G:378binding site for residue GAL G 501
07AC7SOFTWAREASP B:353 , VAL B:354 , TYR B:355 , ASN B:358 , GLY B:359 , TRP B:371 , HIS B:374 , ASN B:378binding site for Poly-Saccharide residues GAL B 501 through NAG B 502
08AC8SOFTWAREASP C:353 , VAL C:354 , TYR C:355 , ASN C:358 , GLY C:359 , LYS C:361 , TRP C:371 , HIS C:374 , ASN C:378 , HOH C:605binding site for Poly-Saccharide residues GAL C 501 through NAG C 502
09AC9SOFTWAREASP D:353 , VAL D:354 , TYR D:355 , ASN D:358 , GLY D:359 , LYS D:361 , TRP D:371 , HIS D:374 , ASN D:378 , HOH D:698 , HOH D:701 , HOH D:702 , HOH D:719 , HOH D:727 , HOH D:736 , HOH D:742binding site for Poly-Saccharide residues GAL D 501 through NAG D 502
10AD1SOFTWAREASP E:353 , VAL E:354 , TYR E:355 , GLY E:359 , LYS E:361 , TRP E:371 , HIS E:374 , ASN E:378 , HOH E:612 , HOH E:731 , HOH E:741binding site for Poly-Saccharide residues GAL E 501 through NAG E 502
11AD2SOFTWAREVAL C:444 , ASP F:353 , VAL F:354 , TYR F:355 , ASN F:358 , GLY F:359 , LYS F:361 , TRP F:371 , HIS F:374 , ASN F:378 , HOH F:612 , HOH F:682 , HOH F:714binding site for Poly-Saccharide residues GAL F 501 through NAG F 502

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:351 -A:373
2A:398 -A:412
3B:351 -B:373
4B:398 -B:412
5C:351 -C:373
6C:398 -C:412
7D:351 -D:373
8D:398 -D:412
9E:351 -E:373
10E:398 -E:412
11F:351 -F:373
12F:398 -F:412
13G:351 -G:373
14G:398 -G:412

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OWL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OWL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OWL)

(-) Exons   (0, 0)

(no "Exon" information available for 4OWL)

(-) 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:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee......eeeeee..........eeeee....hhh.eeee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeee.....eeeee.hhh....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4owl A 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQQ 468
                                   346       356       366       376       386       396       406       416       426       436       446       456       466  


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee..........eeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl B 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466 


Chain C from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee.........eeeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl C 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466 


Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......eeeeee.........eeeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl D 335 SAMAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQQVKL 471
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       


Chain E from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee......eeeeee.........eeeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4owl E 336 AMAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   345       355       365       375       385       395       405       415       425       435       445       455       465  


Chain F from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee..........eeeee....hhhh.eee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl F 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466 


Chain G from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeee.........eeeeee....hhh.eeee.....eee......eeee.....eeee....hhhh.eeee..eeee.........eeeeeee..eeeeee.hhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4owl G 337 MAHVTLQSLSNNDLCLDVYGENGDKTVAGGSVNGWSCHGSWNQVWGLDKEERYRSRVASDRCLTVNADKTLTVEQCGANLAQKWYWEGDKLISRYVDGNNTRYLLNIVGGRNVQVTPENEANQARWKPTLQ 467
                                   346       356       366       376       386       396       406       416       426       436       446       456       466
   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 4OWL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OWL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OWL)

(-) Gene Ontology  (5, 5)

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  4owl
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  VVHA_VIBVU | P19247
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 Related Entries

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

UniProtKB/Swiss-Prot
        VVHA_VIBVU | P19247: 4owj 4owk

(-) Related Entries Specified in the PDB File

4owj SAME PROTEIN WITHOUT LIGANDS BOUND
4owk SAME PROTEIN WITH N-ACETYL-D-GALACTOSAMINE BOUND