2DDSA

Crystal structure of sphingomyelinase from bacillus cereus with cobalt ion
Total Genus 95
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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
95
sequence length
299
structure length
299
Chain Sequence
NDTLKVMTHNVYMLSTNLYPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQTAVLGRSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQYVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAEDSMCGKTSPASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAENNNDSEYASMFKTLNASVPSYTGHTATWDATTNSIAKYNFPDSPAEYLDYIIASKDHANPSYIENKVLQPKSPQWTVTSWFQKYTYNDYSDHYPVEATISM
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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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molecule tags Hydrolase
molecule keywords Sphingomyelin phosphodiesterase
publication title Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus.
pubmed doi rcsb
source organism Bacillus cereus
total genus 95
structure length 299
sequence length 299
chains with identical sequence B, C, D
ec nomenclature ec 3.1.4.12: Sphingomyelin phosphodiesterase.
pdb deposition date 2006-02-02

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03372 Exo_endo_phos Endonuclease/Exonuclease/phosphatase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.60.10.10 Alpha Beta 4-Layer Sandwich Deoxyribonuclease I; Chain A Endonuclease/exonuclease/phosphatase 2ddsA00
3G2CA 1Y21A 2DNJA 4B5FA 3L1WA 3G1KA 5DV4A 4L1ZA 2EI9A 4AWNA 2IMQX 3NGOA 2F2FB 1BIXA 4IEMA 4F1IA 3NGNA 5DV2A 3N9VA 1DNKA 3G3YA 5HT2A 5INPA 3G3CA 3I48A 3G38A 2F1NA 4L20A 1DEWA 5J8NA 3I41A 5INMA 4GYZA 4L1YA 4FPVA 5A7IA 4QH9A 5CFGA 5INNA 4RUWA 2JC4A 3G8VA 2O3CA 5DFIA 2JC5A 1E9NA 2O3HA 4C1RA 5INKA 3G0AA 3I5VA 4QHDA 2A41B 3W2XA 4L21A 2VOAA 4LNDA 1VYBA 1WDUA 4B5MA 2ISIA 3I46A 3NR8A 2A42B 5J3SA 5CFEA 4A9CA 2A40B 1NTFA 2XSWA 4JG3A 2A3ZB 2J63A 2V0RA 1AKOA 3G2DA 5J3ZA 4B5GA 3G00A 3NGQA 4GZ0A 3GA6A 3G4TA 2D1KB 3TEBA 5J3PA 4F1HA 4GZ2A 3FZIA 3MPRA 1I9ZA 3W3DB 4QHEA 5EWTA 2DDTA 1ZWXA 3G6SA 2DDRA 5DFFA 3CJCD 3G91A 4K6LF 1YJHA 1I9YA 4PUQA 5A7JA 5INOA 2DDSA 4F1HB 3DNIA 5INLA 4GEWA 1DE9A 3G0RA 4CMLA 3MTCA 1SR4B 4CMNA 3U8UA 3WCXA 2UYRX 4B5JA 5INQA 3K55A 4B5HA 4GZ1A 1HD7A 5DG0A 4F1RA 2V0SA 5DFJA 1DE8A 1ATND 3W2YA 5J42A 4FVAA 5DFHA 4B5IA 1SI6X
chains in the Genus database with same CATH superfamily
3G2CA 1Y21A 2DNJA 4B5FA 3L1WA 3G1KA 5DV4A 4L1ZA 2EI9A 4AWNA 2IMQX 3NGOA 2F2FB 1BIXA 4IEMA 4F1IA 3NGNA 5DV2A 3N9VA 1DNKA 3G3YA 5HT2A 5INPA 3G3CA 3I48A 3G38A 2F1NA 4L20A 1DEWA 5J8NA 3I41A 5INMA 4GYZA 4L1YA 4FPVA 5A7IA 4QH9A 5CFGA 5INNA 4RUWA 2JC4A 3G8VA 2O3CA 5DFIA 2JC5A 1E9NA 2O3HA 4C1RA 5INKA 3G0AA 3I5VA 4QHDA 2A41B 3W2XA 4L21A 2VOAA 4LNDA 1VYBA 1WDUA 4B5MA 2ISIA 3I46A 3NR8A 2A42B 5J3SA 5CFEA 4A9CA 2A40B 1NTFA 2XSWA 4JG3A 2A3ZB 2J63A 2V0RA 1AKOA 3G2DA 5J3ZA 4B5GA 3G00A 3NGQA 4GZ0A 3GA6A 3G4TA 2D1KB 3TEBA 5J3PA 4F1HA 4GZ2A 3FZIA 3MPRA 1I9ZA 3W3DB 4QHEA 5EWTA 2DDTA 1ZWXA 3G6SA 2DDRA 5DFFA 3CJCD 3G91A 4K6LF 1YJHA 1I9YA 4PUQA 5A7JA 5INOA 2DDSA 4F1HB 3DNIA 5INLA 4GEWA 1DE9A 3G0RA 4CMLA 3MTCA 1SR4B 4CMNA 3U8UA 3WCXA 2UYRX 4B5JA 5INQA 3K55A 4B5HA 4GZ1A 1HD7A 5DG0A 4F1RA 2V0SA 5DFJA 1DE8A 1ATND 3W2YA 5J42A 4FVAA 5DFHA 4B5IA 1SI6X
chains in the Genus database with same CATH topology
3G2CA 1Y21A 2DNJA 4B5FA 3L1WA 3G1KA 5DV4A 4L1ZA 2EI9A 4AWNA 2IMQX 3NGOA 2F2FB 1BIXA 4IEMA 4F1IA 3NGNA 5DV2A 3N9VA 1DNKA 3G3YA 5HT2A 5INPA 3G3CA 3I48A 3G38A 2F1NA 4L20A 1DEWA 5J8NA 3I41A 5INMA 4GYZA 4L1YA 4FPVA 5A7IA 4QH9A 5CFGA 5INNA 4RUWA 2JC4A 3G8VA 2O3CA 5DFIA 2JC5A 1E9NA 2O3HA 4C1RA 5INKA 3G0AA 3I5VA 4QHDA 2A41B 3W2XA 4L21A 2VOAA 4LNDA 1VYBA 1WDUA 4B5MA 2ISIA 3I46A 3NR8A 2A42B 5J3SA 5CFEA 4A9CA 2A40B 1NTFA 2XSWA 4JG3A 2A3ZB 2J63A 2V0RA 1AKOA 3G2DA 5J3ZA 4B5GA 3G00A 3NGQA 4GZ0A 3GA6A 3G4TA 2D1KB 3TEBA 5J3PA 4F1HA 4GZ2A 3FZIA 3MPRA 1I9ZA 3W3DB 4QHEA 5EWTA 2DDTA 1ZWXA 3G6SA 2DDRA 5DFFA 3CJCD 3G91A 4K6LF 1YJHA 1I9YA 4PUQA 5A7JA 5INOA 2DDSA 4F1HB 3DNIA 5INLA 4GEWA 1DE9A 3G0RA 4CMLA 3MTCA 1SR4B 4CMNA 3U8UA 3WCXA 2UYRX 4B5JA 5INQA 3K55A 4B5HA 4GZ1A 1HD7A 5DG0A 4F1RA 2V0SA 5DFJA 1DE8A 1ATND 3W2YA 5J42A 4FVAA 5DFHA 4B5IA 1SI6X
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3G2C A;  1Y21 A;  2DNJ A;  4B5F A;  3L1W A;  3G1K A;  5DV4 A;  4L1Z A;  2EI9 A;  4AWN A;  2IMQ X;  3NGO A;  2F2F B;  1BIX A;  4IEM A;  4F1I A;  3NGN A;  5DV2 A;  3N9V A;  1DNK A;  3G3Y A;  5HT2 A;  5INP A;  3G3C A;  3I48 A;  3G38 A;  2F1N A;  4L20 A;  1DEW A;  5J8N A;  3I41 A;  5INM A;  4GYZ A;  4L1Y A;  4FPV A;  5A7I A;  4QH9 A;  5CFG A;  5INN A;  4RUW A;  2JC4 A;  3G8V A;  2O3C A;  5DFI A;  2JC5 A;  1E9N A;  2O3H A;  4C1R A;  5INK A;  3G0A A;  3I5V A;  4QHD A;  2A41 B;  3W2X A;  4L21 A;  2VOA A;  4LND A;  1VYB A;  1WDU A;  4B5M A;  2ISI A;  3I46 A;  3NR8 A;  2A42 B;  5J3S A;  5CFE A;  4A9C A;  2A40 B;  1NTF A;  2XSW A;  4JG3 A;  2A3Z B;  2J63 A;  2V0R A;  1AKO A;  3G2D A;  5J3Z A;  4B5G A;  3G00 A;  3NGQ A;  4GZ0 A;  3GA6 A;  3G4T A;  2D1K B;  3TEB A;  5J3P A;  4F1H A;  4GZ2 A;  3FZI A;  3MPR A;  1I9Z A;  3W3D B;  4QHE A;  5EWT A;  2DDT A;  1ZWX A;  3G6S A;  2DDR A;  5DFF A;  3CJC D;  3G91 A;  4K6L F;  1YJH A;  1I9Y A;  4PUQ A;  5A7J A;  5INO A;  2DDS A;  4F1H B;  3DNI A;  5INL A;  4GEW A;  1DE9 A;  3G0R A;  4CML A;  3MTC A;  1SR4 B;  4CMN A;  3U8U A;  3WCX A;  2UYR X;  4B5J A;  5INQ A;  3K55 A;  4B5H A;  4GZ1 A;  1HD7 A;  5DG0 A;  4F1R A;  2V0S A;  5DFJ A;  1DE8 A;  1ATN D;  3W2Y A;  5J42 A;  4FVA A;  5DFH A;  4B5I A;  1SI6 X; 
#chains in the Genus database with same CATH topology
 3G2C A;  1Y21 A;  2DNJ A;  4B5F A;  3L1W A;  3G1K A;  5DV4 A;  4L1Z A;  2EI9 A;  4AWN A;  2IMQ X;  3NGO A;  2F2F B;  1BIX A;  4IEM A;  4F1I A;  3NGN A;  5DV2 A;  3N9V A;  1DNK A;  3G3Y A;  5HT2 A;  5INP A;  3G3C A;  3I48 A;  3G38 A;  2F1N A;  4L20 A;  1DEW A;  5J8N A;  3I41 A;  5INM A;  4GYZ A;  4L1Y A;  4FPV A;  5A7I A;  4QH9 A;  5CFG A;  5INN A;  4RUW A;  2JC4 A;  3G8V A;  2O3C A;  5DFI A;  2JC5 A;  1E9N A;  2O3H A;  4C1R A;  5INK A;  3G0A A;  3I5V A;  4QHD A;  2A41 B;  3W2X A;  4L21 A;  2VOA A;  4LND A;  1VYB A;  1WDU A;  4B5M A;  2ISI A;  3I46 A;  3NR8 A;  2A42 B;  5J3S A;  5CFE A;  4A9C A;  2A40 B;  1NTF A;  2XSW A;  4JG3 A;  2A3Z B;  2J63 A;  2V0R A;  1AKO A;  3G2D A;  5J3Z A;  4B5G A;  3G00 A;  3NGQ A;  4GZ0 A;  3GA6 A;  3G4T A;  2D1K B;  3TEB A;  5J3P A;  4F1H A;  4GZ2 A;  3FZI A;  3MPR A;  1I9Z A;  3W3D B;  4QHE A;  5EWT A;  2DDT A;  1ZWX A;  3G6S A;  2DDR A;  5DFF A;  3CJC D;  3G91 A;  4K6L F;  1YJH A;  1I9Y A;  4PUQ A;  5A7J A;  5INO A;  2DDS A;  4F1H B;  3DNI A;  5INL A;  4GEW A;  1DE9 A;  3G0R A;  4CML A;  3MTC A;  1SR4 B;  4CMN A;  3U8U A;  3WCX A;  2UYR X;  4B5J A;  5INQ A;  3K55 A;  4B5H A;  4GZ1 A;  1HD7 A;  5DG0 A;  4F1R A;  2V0S A;  5DFJ A;  1DE8 A;  1ATN D;  3W2Y A;  5J42 A;  4FVA A;  5DFH A;  4B5I A;  1SI6 X; 
#chains in the Genus database with same CATH homology
 3G2C A;  1Y21 A;  2DNJ A;  4B5F A;  3L1W A;  3G1K A;  5DV4 A;  4L1Z A;  2EI9 A;  4AWN A;  2IMQ X;  3NGO A;  2F2F B;  1BIX A;  4IEM A;  4F1I A;  3NGN A;  5DV2 A;  3N9V A;  1DNK A;  3G3Y A;  5HT2 A;  5INP A;  3G3C A;  3I48 A;  3G38 A;  2F1N A;  4L20 A;  1DEW A;  5J8N A;  3I41 A;  5INM A;  4GYZ A;  4L1Y A;  4FPV A;  5A7I A;  4QH9 A;  5CFG A;  5INN A;  4RUW A;  2JC4 A;  3G8V A;  2O3C A;  5DFI A;  2JC5 A;  1E9N A;  2O3H A;  4C1R A;  5INK A;  3G0A A;  3I5V A;  4QHD A;  2A41 B;  3W2X A;  4L21 A;  2VOA A;  4LND A;  1VYB A;  1WDU A;  4B5M A;  2ISI A;  3I46 A;  3NR8 A;  2A42 B;  5J3S A;  5CFE A;  4A9C A;  2A40 B;  1NTF A;  2XSW A;  4JG3 A;  2A3Z B;  2J63 A;  2V0R A;  1AKO A;  3G2D A;  5J3Z A;  4B5G A;  3G00 A;  3NGQ A;  4GZ0 A;  3GA6 A;  3G4T A;  2D1K B;  3TEB A;  5J3P A;  4F1H A;  4GZ2 A;  3FZI A;  3MPR A;  1I9Z A;  3W3D B;  4QHE A;  5EWT A;  2DDT A;  1ZWX A;  3G6S A;  2DDR A;  5DFF A;  3CJC D;  3G91 A;  4K6L F;  1YJH A;  1I9Y A;  4PUQ A;  5A7J A;  5INO A;  2DDS A;  4F1H B;  3DNI A;  5INL A;  4GEW A;  1DE9 A;  3G0R A;  4CML A;  3MTC A;  1SR4 B;  4CMN A;  3U8U A;  3WCX A;  2UYR X;  4B5J A;  5INQ A;  3K55 A;  4B5H A;  4GZ1 A;  1HD7 A;  5DG0 A;  4F1R A;  2V0S A;  5DFJ A;  1DE8 A;  1ATN D;  3W2Y A;  5J42 A;  4FVA A;  5DFH A;  4B5I A;  1SI6 X; 
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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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