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


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