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


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