4P1YB

Crystal structure of staphylococcal gamma-hemolysin prepore
Total Genus 59
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
59
sequence length
275
structure length
264
Chain Sequence
DIGQGAEIIKRTQDITSKRLAITQNIQFDFVKDKKYNKDALVVKMQGFISSRTTYSDLKKYPYIKRMIWPFQYNISLKTKDSNVDLINYLPKNKIDSADVSQKLGYNIGSGSFNYSKTISYNQKNYVTEVESQNSKGVKWGVKANSFVTPNGQVSAYDQYLFAQDPTGPAARDYFVPDNQLPPLIQSGFNPSFITTLSHERGKGDKSEFEITYGRNMDATYAYVTRHRLAVDRKHDAFKNRNVTVKYEVNWKTHEVKIKSITPK
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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publication title Molecular basis of transmembrane beta-barrel formation of staphylococcal pore-forming toxins.
pubmed doi rcsb
molecule tags Toxin
source organism Staphylococcus aureus
molecule keywords Gamma-hemolysin component B
total genus 59
structure length 264
sequence length 275
chains with identical sequence D, F, H
ec nomenclature
pdb deposition date 2014-02-28

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF07968 Leukocidin Leukocidin/Hemolysin toxin family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.70.240.10 Mainly Beta Distorted Sandwich Leukocidin-like Leukocidin/porin MspA 4p1yB00
2YGTA 4IYAA 3M2LA 4I0NA 4IYCA 4P1YA 4H56A 4P24A 3ANZA 2QK7A 5K59C 7AHLA 1PVLA 4IZLA 4IDJA 3O44A 3B07B 3ROHA 1T5RA 4P1XB 4IYTA 4TW1B 3B07A 4YHDA 4TW1A 4U6VA 4P1XA 4J0OA 1LKFA 5K59A 3M4DA 4Q7GA 3M4EA 4P1YB 3LKFA 2LKFA 3M3RA 2QK7B
chains in the Genus database with same CATH superfamily
2YGTA 4IYAA 3M2LA 4I0NA 4IYCA 4P1YA 4H56A 4P24A 3ANZA 2QK7A 5K59C 7AHLA 1PVLA 4IZLA 4IDJA 3O44A 3B07B 3ROHA 1T5RA 4P1XB 4IYTA 4TW1B 3B07A 4YHDA 1XEZA 4TW1A 4U6VA 4P1XA 4J0OA 1LKFA 5K59A 3M4DA 4Q7GA 3M4EA 4P1YB 3LKFA 2LKFA 3M3RA 2QK7B
chains in the Genus database with same CATH topology
2YGTA 4IYAA 3M2LA 4I0NA 4IYCA 4P1YA 4H56A 4P24A 3ANZA 2QK7A 5K59C 7AHLA 1PVLA 4IZLA 4IDJA 3O44A 3B07B 3ROHA 1T5RA 4P1XB 4IYTA 4TW1B 3B07A 4YHDA 4TW1A 4U6VA 4P1XA 4J0OA 1LKFA 5K59A 3M4DA 4Q7GA 3M4EA 4P1YB 3LKFA 2LKFA 3M3RA 2QK7B
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2YGT A;  4IYA A;  3M2L A;  4I0N A;  4IYC A;  4P1Y A;  4H56 A;  4P24 A;  3ANZ A;  2QK7 A;  5K59 C;  7AHL A;  1PVL A;  4IZL A;  4IDJ A;  3O44 A;  3B07 B;  3ROH A;  1T5R A;  4P1X B;  4IYT A;  4TW1 B;  3B07 A;  4YHD A;  4TW1 A;  4U6V A;  4P1X A;  4J0O A;  1LKF A;  5K59 A;  3M4D A;  4Q7G A;  3M4E A;  4P1Y B;  3LKF A;  2LKF A;  3M3R A;  2QK7 B; 
#chains in the Genus database with same CATH topology
 2YGT A;  4IYA A;  3M2L A;  4I0N A;  4IYC A;  4P1Y A;  4H56 A;  4P24 A;  3ANZ A;  2QK7 A;  5K59 C;  7AHL A;  1PVL A;  4IZL A;  4IDJ A;  3O44 A;  3B07 B;  3ROH A;  1T5R A;  4P1X B;  4IYT A;  4TW1 B;  3B07 A;  4YHD A;  1XEZ A;  4TW1 A;  4U6V A;  4P1X A;  4J0O A;  1LKF A;  5K59 A;  3M4D A;  4Q7G A;  3M4E A;  4P1Y B;  3LKF A;  2LKF A;  3M3R A;  2QK7 B; 
#chains in the Genus database with same CATH homology
 2YGT A;  4IYA A;  3M2L A;  4I0N A;  4IYC A;  4P1Y A;  4H56 A;  4P24 A;  3ANZ A;  2QK7 A;  5K59 C;  7AHL A;  1PVL A;  4IZL A;  4IDJ A;  3O44 A;  3B07 B;  3ROH A;  1T5R A;  4P1X B;  4IYT A;  4TW1 B;  3B07 A;  4YHD A;  4TW1 A;  4U6V A;  4P1X A;  4J0O A;  1LKF A;  5K59 A;  3M4D A;  4Q7G A;  3M4E A;  4P1Y B;  3LKF A;  2LKF A;  3M3R A;  2QK7 B; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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