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.

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


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