4B28A

Crystal structure of dmsp lyase rddddp from roseobacter denitrificans
Total Genus 149
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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
149
sequence length
437
structure length
437
Chain Sequence
RKIDPSRGATLGDGSPNDMNRVEIGPTQLAFAEWHTARLDLPDLAAMRRFRHRRLTDHVVARGYAGLLMFDPLNIRYATDSTNMQLWNTHNPFRATLLCADGYMVMWDYKNSPFLSEFNPLVREQRAGADLFYFDRGDKVDVAADVFANEVRILLRDHAPGLRRLAVDKVMLHGLRALQAQGFEIMDGEEVTEKARSVKGPDEIRAMRCASHACEVAVRKMEDFARSKVGDGVTCENDIWAILHSENVRRGGEWIETRLLASGPRSNPWFQECGPRVCQRNEIISFDTDLVGAYGICTDISRSWWIGDQKPRADMIYAMQHGVEHIRTNMEMLKPGVMIPELSANTHVLDAKFQKQKYGCLMHGVGLCDEWPLVAYPDHAVAGAYDYPLEPGMTLCVEALISEEGGDFSIKLEDQVLITEDGYENLTKYPFDPALMG
Loading diagram...

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.

publication title The Structure of Rddddp from Roseobacter Denitrificans Reveals that Dmsp Lyases in the Dddp-Family are Metalloenzymes.
pubmed doi rcsb
source organism Roseobacter denitrificans och 114
molecule tags Lyase
molecule keywords METALLOPEPTIDASE, FAMILY M24, PUTATIVE
total genus 149
structure length 437
sequence length 437
ec nomenclature ec 4.4.1.3: Dimethylpropiothetin dethiomethylase.
pdb deposition date 2012-07-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00557 Peptidase_M24 Metallopeptidase family M24
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.350.10 Alpha Beta 3-Layer(aba) Sandwich Creatine Amidinohydrolase; Chain A, domain 1 Creatinase/prolidase N-terminal domain 4b28A01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4b28A02
4IKUA 3CB5A 2EVCA 4U6EA 5CDVA 3PN9A 2B3KA 2OAZA 3TB5A 2OKNA 2V3ZA 2ZSGA 4S2TP 1W2MA 5D6EA 3PKDA 4B28A 2B3HA 2BWUA 2GZ5A 4U69A 2GU5A 4ZNGA 1WL6A 4S00A 2ADUA 3FMQA 5D6FA 4IECA 1XGNA 2Q92A 3CTZA 2BWSA 1N51A 4IKSA 4PV4A 2G6PA 5JFRA 5CDLA 2EA4A 2GGBA 3BITA 4ZWOA 3RVAA 2DFIA 3IL0A 1KQ9A 3BIPA 1YJ3A 2NQ6A 2Q8KA 5FCHA 3MX6A 3S6BA 3OOOA 4FLLA 4JUQA 5CE6A 4IPAA 1C27A 3TAVA 3CB6A 2P98A 3PKBA 1WL9A 4IF7A 3FMRA 1XGMA 2GG0A 1R5GA 4IKRA 4EGEA 4OOKA 3PEBA 2BWWA 5CDEA 1WY2A 2BHDA 2GG3A 3FM3A 4KM3A 2BHCA 1QXYA 2BHBA 2BWVA 1XGOA 4A6VA 4U73A 2P99A 3IU8A 1XNZA 1M35A 3OVKA 2BHAA 4IU6A 1C21A 5E5BA 4R60A 3O5VA 3L24A 2Q94A 4U76A 2GG2A 2P9AA 3D27A 2BN7A 2BWYA 1WKMA 2EVOA 4PNCA 2GTXA 1QZYA 4HXXA 4RZYA 2V3YA 2GG7A 4U71A 4ZWPA 1YVMA 4FO8A 2IW2A 1C22A 4U75A 2Q95A 1XGSA 1YW8A 4U6WA 4U1BA 2GU4A 4RZZA 3I7MA 5FCFA 2GA2A 2NQ7A 1YW7A 1KQ0A 3IU9A 1CHMA 3L7GA 4QR8A 3MATA 3PKEA 4FLJA 2BB7A 5JI6A 1B59A 2GGCA 1QXZA 4MATA 4U6ZA 4FO7A 4ZWUA 3MR1A 2V3XA 3QOCA 3PKCA 1YW9A 3Q6DA 4FLKA 4IDYA 4U70A 4U6JA 4Z7MA 4FKCA 4FUKA 1Y1NA 2EA2A 4IKTA 2GG9A 1MATA 2GU7A 1O0XA 1R5HA 2HOWA 5CIKA 3RORA 5JHUA 4S01A 4RGZ1 2V6CA 1WN1A 1WLRA 3IU7A 2B3LA 4FLIA 1R58A 1QXWA 1C23A 2EVMA 5E2CA 2Q93A 4U6CA 1BN5A 1W7VA 1C24A 1JAWA 2GG8A 2GG5A 2Q96A 2MATA 1A16A 4S2RP 1PV9A 1BOAA 1WBQA 5CLSA 3BIQA 2GU6A 2BH3A 4A6WA 1KP0A 3IG4A 2BWTA 1B6AA 2BWXA 3PKAA 5CNXA
chains in the Genus database with same CATH superfamily
4IKUA 3CB5A 2EVCA 4U6EA 5CDVA 3PN9A 2B3KA 2OAZA 3TB5A 2OKNA 2V3ZA 2ZSGA 4S2TP 1W2MA 5D6EA 3PKDA 4B28A 2B3HA 2BWUA 2GZ5A 4U69A 2GU5A 4ZNGA 1WL6A 4S00A 2ADUA 3FMQA 5D6FA 4IECA 1XGNA 2Q92A 3CTZA 2BWSA 1N51A 4IKSA 4PV4A 2G6PA 5JFRA 5CDLA 2EA4A 2GGBA 3BITA 4ZWOA 3RVAA 2DFIA 3IL0A 1KQ9A 3BIPA 1YJ3A 2NQ6A 2Q8KA 5FCHA 3MX6A 3S6BA 3OOOA 4FLLA 4JUQA 5CE6A 4IPAA 1C27A 3TAVA 3CB6A 2P98A 3PKBA 1WL9A 4IF7A 3FMRA 1XGMA 2GG0A 1R5GA 4IKRA 4EGEA 4OOKA 3PEBA 2BWWA 5CDEA 1WY2A 2BHDA 2GG3A 3FM3A 4KM3A 2BHCA 1QXYA 2BHBA 2BWVA 1XGOA 4A6VA 4U73A 2P99A 3IU8A 1XNZA 1M35A 3OVKA 2BHAA 4IU6A 1C21A 5E5BA 4R60A 3O5VA 3L24A 2Q94A 4U76A 2GG2A 2P9AA 3D27A 2BN7A 2BWYA 1WKMA 2EVOA 4PNCA 2GTXA 1QZYA 4HXXA 4RZYA 2V3YA 2GG7A 4U71A 4ZWPA 1YVMA 4FO8A 2IW2A 1C22A 4U75A 2Q95A 1XGSA 1YW8A 4U6WA 4U1BA 2GU4A 4RZZA 3I7MA 5FCFA 2GA2A 2NQ7A 1YW7A 1KQ0A 3IU9A 1CHMA 3L7GA 4QR8A 3MATA 3PKEA 4FLJA 2BB7A 5JI6A 1B59A 2GGCA 1QXZA 4MATA 4U6ZA 4FO7A 4ZWUA 3MR1A 2V3XA 3QOCA 3PKCA 1YW9A 3Q6DA 4FLKA 4IDYA 4U70A 4U6JA 4Z7MA 4FKCA 4FUKA 1Y1NA 2EA2A 4IKTA 2GG9A 1MATA 2GU7A 1O0XA 1R5HA 2HOWA 5CIKA 3RORA 5JHUA 4S01A 4RGZ1 2V6CA 1WN1A 1WLRA 3IU7A 2B3LA 4FLIA 1R58A 1QXWA 1C23A 2EVMA 5E2CA 2Q93A 4U6CA 1BN5A 1W7VA 1C24A 1JAWA 2GG8A 2GG5A 2Q96A 2MATA 1A16A 4S2RP 1PV9A 1BOAA 1WBQA 5CLSA 3BIQA 2GU6A 2BH3A 4A6WA 1KP0A 3IG4A 2BWTA 1B6AA 2BWXA 3PKAA 5CNXA
chains in the Genus database with same CATH topology
4IKUA 3CB5A 2EVCA 4U6EA 5CDVA 3PN9A 2B3KA 2OAZA 3TB5A 2OKNA 2V3ZA 2ZSGA 4S2TP 1W2MA 5D6EA 3PKDA 4B28A 2B3HA 2BWUA 2GZ5A 4U69A 2GU5A 4ZNGA 1WL6A 4S00A 2ADUA 3FMQA 5D6FA 4IECA 1XGNA 2Q92A 3CTZA 2BWSA 1N51A 4IKSA 4PV4A 2G6PA 5JFRA 5CDLA 2EA4A 2GGBA 3BITA 4ZWOA 3RVAA 2DFIA 3IL0A 1KQ9A 3BIPA 1YJ3A 2NQ6A 2Q8KA 5FCHA 3MX6A 3S6BA 3OOOA 4FLLA 4JUQA 5CE6A 4IPAA 1C27A 3TAVA 3CB6A 2P98A 3PKBA 1WL9A 4IF7A 3FMRA 1XGMA 2GG0A 1R5GA 4IKRA 4EGEA 4OOKA 3PEBA 2BWWA 5CDEA 1WY2A 2BHDA 2GG3A 3FM3A 4KM3A 2BHCA 1QXYA 2BHBA 2BWVA 1XGOA 4A6VA 4U73A 2P99A 3IU8A 1XNZA 1M35A 3OVKA 2BHAA 4IU6A 1C21A 5E5BA 4R60A 3O5VA 3L24A 2Q94A 4U76A 2GG2A 2P9AA 3D27A 2BN7A 2BWYA 1WKMA 2EVOA 4PNCA 2GTXA 1QZYA 4HXXA 4RZYA 2V3YA 2GG7A 4U71A 4ZWPA 1YVMA 4FO8A 2IW2A 1C22A 4U75A 2Q95A 1XGSA 1YW8A 4U6WA 4U1BA 2GU4A 4RZZA 3I7MA 5FCFA 2GA2A 2NQ7A 1YW7A 1KQ0A 3IU9A 1CHMA 3L7GA 4QR8A 3MATA 3PKEA 4FLJA 2BB7A 5JI6A 1B59A 2GGCA 1QXZA 4MATA 4U6ZA 4FO7A 4ZWUA 3MR1A 2V3XA 3QOCA 3PKCA 1YW9A 3Q6DA 4FLKA 4IDYA 4U70A 4U6JA 4Z7MA 4FKCA 4FUKA 1Y1NA 2EA2A 4IKTA 2GG9A 1MATA 2GU7A 1O0XA 1R5HA 2HOWA 5CIKA 3RORA 5JHUA 4S01A 4RGZ1 2V6CA 1WN1A 1WLRA 3IU7A 2B3LA 4FLIA 1R58A 1QXWA 1C23A 2EVMA 5E2CA 2Q93A 4U6CA 1BN5A 1W7VA 1C24A 1JAWA 2GG8A 2GG5A 2Q96A 2MATA 1A16A 4S2RP 1PV9A 1BOAA 1WBQA 5CLSA 3BIQA 2GU6A 2BH3A 4A6WA 1KP0A 3IG4A 2BWTA 1B6AA 2BWXA 3PKAA 5CNXA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4IKU A;  3CB5 A;  2EVC A;  4U6E A;  5CDV A;  3PN9 A;  2B3K A;  2OAZ A;  3TB5 A;  2OKN A;  2V3Z A;  2ZSG A;  4S2T P;  1W2M A;  5D6E A;  3PKD A;  4B28 A;  2B3H A;  2BWU A;  2GZ5 A;  4U69 A;  2GU5 A;  4ZNG A;  1WL6 A;  4S00 A;  2ADU A;  3FMQ A;  5D6F A;  4IEC A;  1XGN A;  2Q92 A;  3CTZ A;  2BWS A;  1N51 A;  4IKS A;  4PV4 A;  2G6P A;  5JFR A;  5CDL A;  2EA4 A;  2GGB A;  3BIT A;  4ZWO A;  3RVA A;  2DFI A;  3IL0 A;  1KQ9 A;  3BIP A;  1YJ3 A;  2NQ6 A;  2Q8K A;  5FCH A;  3MX6 A;  3S6B A;  3OOO A;  4FLL A;  4JUQ A;  5CE6 A;  4IPA A;  1C27 A;  3TAV A;  3CB6 A;  2P98 A;  3PKB A;  1WL9 A;  4IF7 A;  3FMR A;  1XGM A;  2GG0 A;  1R5G A;  4IKR A;  4EGE A;  4OOK A;  3PEB A;  2BWW A;  5CDE A;  1WY2 A;  2BHD A;  2GG3 A;  3FM3 A;  4KM3 A;  2BHC A;  1QXY A;  2BHB A;  2BWV A;  1XGO A;  4A6V A;  4U73 A;  2P99 A;  3IU8 A;  1XNZ A;  1M35 A;  3OVK A;  2BHA A;  4IU6 A;  1C21 A;  5E5B A;  4R60 A;  3O5V A;  3L24 A;  2Q94 A;  4U76 A;  2GG2 A;  2P9A A;  3D27 A;  2BN7 A;  2BWY A;  1WKM A;  2EVO A;  4PNC A;  2GTX A;  1QZY A;  4HXX A;  4RZY A;  2V3Y A;  2GG7 A;  4U71 A;  4ZWP A;  1YVM A;  4FO8 A;  2IW2 A;  1C22 A;  4U75 A;  2Q95 A;  1XGS A;  1YW8 A;  4U6W A;  4U1B A;  2GU4 A;  4RZZ A;  3I7M A;  5FCF A;  2GA2 A;  2NQ7 A;  1YW7 A;  1KQ0 A;  3IU9 A;  1CHM A;  3L7G A;  4QR8 A;  3MAT A;  3PKE A;  4FLJ A;  2BB7 A;  5JI6 A;  1B59 A;  2GGC A;  1QXZ A;  4MAT A;  4U6Z A;  4FO7 A;  4ZWU A;  3MR1 A;  2V3X A;  3QOC A;  3PKC A;  1YW9 A;  3Q6D A;  4FLK A;  4IDY A;  4U70 A;  4U6J A;  4Z7M A;  4FKC A;  4FUK A;  1Y1N A;  2EA2 A;  4IKT A;  2GG9 A;  1MAT A;  2GU7 A;  1O0X A;  1R5H A;  2HOW A;  5CIK A;  3ROR A;  5JHU A;  4S01 A;  4RGZ 1;  2V6C A;  1WN1 A;  1WLR A;  3IU7 A;  2B3L A;  4FLI A;  1R58 A;  1QXW A;  1C23 A;  2EVM A;  5E2C A;  2Q93 A;  4U6C A;  1BN5 A;  1W7V A;  1C24 A;  1JAW A;  2GG8 A;  2GG5 A;  2Q96 A;  2MAT A;  1A16 A;  4S2R P;  1PV9 A;  1BOA A;  1WBQ A;  5CLS A;  3BIQ A;  2GU6 A;  2BH3 A;  4A6W A;  1KP0 A;  3IG4 A;  2BWT A;  1B6A A;  2BWX A;  3PKA A;  5CNX A; 
#chains in the Genus database with same CATH topology
 4IKU A;  3CB5 A;  2EVC A;  4U6E A;  5CDV A;  3PN9 A;  2B3K A;  2OAZ A;  3TB5 A;  2OKN A;  2V3Z A;  2ZSG A;  4S2T P;  1W2M A;  5D6E A;  3PKD A;  4B28 A;  2B3H A;  2BWU A;  2GZ5 A;  4U69 A;  2GU5 A;  4ZNG A;  1WL6 A;  4S00 A;  2ADU A;  3FMQ A;  5D6F A;  4IEC A;  1XGN A;  2Q92 A;  3CTZ A;  2BWS A;  1N51 A;  4IKS A;  4PV4 A;  2G6P A;  5JFR A;  5CDL A;  2EA4 A;  2GGB A;  3BIT A;  4ZWO A;  3RVA A;  2DFI A;  3IL0 A;  1KQ9 A;  3BIP A;  1YJ3 A;  2NQ6 A;  2Q8K A;  5FCH A;  3MX6 A;  3S6B A;  3OOO A;  4FLL A;  4JUQ A;  5CE6 A;  4IPA A;  1C27 A;  3TAV A;  3CB6 A;  2P98 A;  3PKB A;  1WL9 A;  4IF7 A;  3FMR A;  1XGM A;  2GG0 A;  1R5G A;  4IKR A;  4EGE A;  4OOK A;  3PEB A;  2BWW A;  5CDE A;  1WY2 A;  2BHD A;  2GG3 A;  3FM3 A;  4KM3 A;  2BHC A;  1QXY A;  2BHB A;  2BWV A;  1XGO A;  4A6V A;  4U73 A;  2P99 A;  3IU8 A;  1XNZ A;  1M35 A;  3OVK A;  2BHA A;  4IU6 A;  1C21 A;  5E5B A;  4R60 A;  3O5V A;  3L24 A;  2Q94 A;  4U76 A;  2GG2 A;  2P9A A;  3D27 A;  2BN7 A;  2BWY A;  1WKM A;  2EVO A;  4PNC A;  2GTX A;  1QZY A;  4HXX A;  4RZY A;  2V3Y A;  2GG7 A;  4U71 A;  4ZWP A;  1YVM A;  4FO8 A;  2IW2 A;  1C22 A;  4U75 A;  2Q95 A;  1XGS A;  1YW8 A;  4U6W A;  4U1B A;  2GU4 A;  4RZZ A;  3I7M A;  5FCF A;  2GA2 A;  2NQ7 A;  1YW7 A;  1KQ0 A;  3IU9 A;  1CHM A;  3L7G A;  4QR8 A;  3MAT A;  3PKE A;  4FLJ A;  2BB7 A;  5JI6 A;  1B59 A;  2GGC A;  1QXZ A;  4MAT A;  4U6Z A;  4FO7 A;  4ZWU A;  3MR1 A;  2V3X A;  3QOC A;  3PKC A;  1YW9 A;  3Q6D A;  4FLK A;  4IDY A;  4U70 A;  4U6J A;  4Z7M A;  4FKC A;  4FUK A;  1Y1N A;  2EA2 A;  4IKT A;  2GG9 A;  1MAT A;  2GU7 A;  1O0X A;  1R5H A;  2HOW A;  5CIK A;  3ROR A;  5JHU A;  4S01 A;  4RGZ 1;  2V6C A;  1WN1 A;  1WLR A;  3IU7 A;  2B3L A;  4FLI A;  1R58 A;  1QXW A;  1C23 A;  2EVM A;  5E2C A;  2Q93 A;  4U6C A;  1BN5 A;  1W7V A;  1C24 A;  1JAW A;  2GG8 A;  2GG5 A;  2Q96 A;  2MAT A;  1A16 A;  4S2R P;  1PV9 A;  1BOA A;  1WBQ A;  5CLS A;  3BIQ A;  2GU6 A;  2BH3 A;  4A6W A;  1KP0 A;  3IG4 A;  2BWT A;  1B6A A;  2BWX A;  3PKA A;  5CNX A; 
#chains in the Genus database with same CATH homology
 4IKU A;  3CB5 A;  2EVC A;  4U6E A;  5CDV A;  3PN9 A;  2B3K A;  2OAZ A;  3TB5 A;  2OKN A;  2V3Z A;  2ZSG A;  4S2T P;  1W2M A;  5D6E A;  3PKD A;  4B28 A;  2B3H A;  2BWU A;  2GZ5 A;  4U69 A;  2GU5 A;  4ZNG A;  1WL6 A;  4S00 A;  2ADU A;  3FMQ A;  5D6F A;  4IEC A;  1XGN A;  2Q92 A;  3CTZ A;  2BWS A;  1N51 A;  4IKS A;  4PV4 A;  2G6P A;  5JFR A;  5CDL A;  2EA4 A;  2GGB A;  3BIT A;  4ZWO A;  3RVA A;  2DFI A;  3IL0 A;  1KQ9 A;  3BIP A;  1YJ3 A;  2NQ6 A;  2Q8K A;  5FCH A;  3MX6 A;  3S6B A;  3OOO A;  4FLL A;  4JUQ A;  5CE6 A;  4IPA A;  1C27 A;  3TAV A;  3CB6 A;  2P98 A;  3PKB A;  1WL9 A;  4IF7 A;  3FMR A;  1XGM A;  2GG0 A;  1R5G A;  4IKR A;  4EGE A;  4OOK A;  3PEB A;  2BWW A;  5CDE A;  1WY2 A;  2BHD A;  2GG3 A;  3FM3 A;  4KM3 A;  2BHC A;  1QXY A;  2BHB A;  2BWV A;  1XGO A;  4A6V A;  4U73 A;  2P99 A;  3IU8 A;  1XNZ A;  1M35 A;  3OVK A;  2BHA A;  4IU6 A;  1C21 A;  5E5B A;  4R60 A;  3O5V A;  3L24 A;  2Q94 A;  4U76 A;  2GG2 A;  2P9A A;  3D27 A;  2BN7 A;  2BWY A;  1WKM A;  2EVO A;  4PNC A;  2GTX A;  1QZY A;  4HXX A;  4RZY A;  2V3Y A;  2GG7 A;  4U71 A;  4ZWP A;  1YVM A;  4FO8 A;  2IW2 A;  1C22 A;  4U75 A;  2Q95 A;  1XGS A;  1YW8 A;  4U6W A;  4U1B A;  2GU4 A;  4RZZ A;  3I7M A;  5FCF A;  2GA2 A;  2NQ7 A;  1YW7 A;  1KQ0 A;  3IU9 A;  1CHM A;  3L7G A;  4QR8 A;  3MAT A;  3PKE A;  4FLJ A;  2BB7 A;  5JI6 A;  1B59 A;  2GGC A;  1QXZ A;  4MAT A;  4U6Z A;  4FO7 A;  4ZWU A;  3MR1 A;  2V3X A;  3QOC A;  3PKC A;  1YW9 A;  3Q6D A;  4FLK A;  4IDY A;  4U70 A;  4U6J A;  4Z7M A;  4FKC A;  4FUK A;  1Y1N A;  2EA2 A;  4IKT A;  2GG9 A;  1MAT A;  2GU7 A;  1O0X A;  1R5H A;  2HOW A;  5CIK A;  3ROR A;  5JHU A;  4S01 A;  4RGZ 1;  2V6C A;  1WN1 A;  1WLR A;  3IU7 A;  2B3L A;  4FLI A;  1R58 A;  1QXW A;  1C23 A;  2EVM A;  5E2C A;  2Q93 A;  4U6C A;  1BN5 A;  1W7V A;  1C24 A;  1JAW A;  2GG8 A;  2GG5 A;  2Q96 A;  2MAT A;  1A16 A;  4S2R P;  1PV9 A;  1BOA A;  1WBQ A;  5CLS A;  3BIQ A;  2GU6 A;  2BH3 A;  4A6W A;  1KP0 A;  3IG4 A;  2BWT A;  1B6A A;  2BWX A;  3PKA A;  5CNX 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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