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
4J0OA 1T5RA 3LKFA 4TW1B 4P1YB 4H56A 3ANZA 4IDJA 3B07A 4YHDA 5K59C 1PVLA 4IYCA 4U6VA 3O44A 4IZLA 4IYTA 4P1YA 3ROHA 2YGTA 4P1XA 4Q7GA 2QK7A 3M2LA 4IYAA 3M4DA 4P1XB 1LKFA 4TW1A 3B07B 5K59A 3M4EA 2LKFA 7AHLA 3M3RA 2QK7B 4P24A 4I0NA
chains in the Genus database with same CATH superfamily
4J0OA 1T5RA 3LKFA 4TW1B 4P1YB 4H56A 3ANZA 4IDJA 3B07A 4YHDA 5K59C 1PVLA 4IYCA 4U6VA 3O44A 4IZLA 4IYTA 4P1YA 3ROHA 2YGTA 4P1XA 4Q7GA 2QK7A 3M2LA 1XEZA 4IYAA 3M4DA 4P1XB 1LKFA 4TW1A 3B07B 5K59A 3M4EA 2LKFA 7AHLA 3M3RA 2QK7B 4P24A 4I0NA
chains in the Genus database with same CATH topology
4J0OA 1T5RA 3LKFA 4TW1B 4P1YB 4H56A 3ANZA 4IDJA 3B07A 4YHDA 5K59C 1PVLA 4IYCA 4U6VA 3O44A 4IZLA 4IYTA 4P1YA 3ROHA 2YGTA 4P1XA 4Q7GA 2QK7A 3M2LA 4IYAA 3M4DA 4P1XB 1LKFA 4TW1A 3B07B 5K59A 3M4EA 2LKFA 7AHLA 3M3RA 2QK7B 4P24A 4I0NA
chains in the Genus database with same CATH homology


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