4RZYA

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp in complex with mes
Total Genus 157
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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
157
sequence length
439
structure length
439
Chain Sequence
RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKYGCLMHGVGLCDEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA
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 Peptidase M24
publication title Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.
pubmed doi rcsb
source organism Silicibacter lacuscaerulensis
molecule tags Lyase
total genus 157
structure length 439
sequence length 439
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2014-12-26

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 4rzyA01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4rzyA02
5E2CA 4U6JA 4U6CA 1XGNA 1C22A 2BWWA 1C23A 2B3HA 3FM3A 4A6VA 3BITA 3QOCA 4FLIA 4ZWOA 2GTXA 4IU6A 3Q6DA 4EGEA 4ZWPA 5D6FA 1M35A 2P98A 1KQ9A 2EA2A 4IPAA 1QXZA 2GU4A 3O5VA 2EVOA 2GU5A 1XGOA 3MATA 3PN9A 3RVAA 3PKEA 5E5BA 3CB6A 1R5HA 1QXWA 2ADUA 3IG4A 5D6EA 3PKBA 2BH3A 1BOAA 2BB7A 5FCHA 2BHDA 1XGMA 2G6PA 4JUQA 3IU8A 4FLLA 1YW7A 2GG3A 4ZWUA 3IU7A 2GG2A 4U6EA 2ZSGA 2GA2A 2OAZA 4PNCA 2BWVA 2DFIA 2BHBA 1YW9A 1BN5A 4U76A 2MATA 4A6WA 2BWUA 1B59A 5CDLA 3CTZA 2BHCA 1QZYA 3FMQA 4IKRA 1B6AA 2Q8KA 1R58A 4U75A 1WL9A 2P99A 1N51A 1WY2A 1YJ3A 1W2MA 2BN7A 2B3LA 2EVMA 5CDVA 5JHUA 2NQ6A 3TB5A 1WKMA 4IKUA 3PKDA 4U1BA 2BHAA 2GG5A 4PV4A 4HXXA 2B3KA 2BWYA 4MATA 5CDEA 3I7MA 3CB5A 4IKSA 1C27A 4RZZA 4RGZ1 2V3ZA 3IL0A 4U70A 2HOWA 4U71A 5CE6A 4S2RP 4IKTA 1WBQA 1JAWA 4B28A 3D27A 2GGBA 4FO7A 2GG0A 2Q94A 4ZNGA 3MR1A 4FUKA 4OOKA 3MX6A 2EA4A 1W7VA 4S01A 1PV9A 4IECA 4RZYA 2V3YA 2NQ7A 3S6BA 1KP0A 2BWXA 3L24A 3IU9A 1O0XA 4IF7A 3PEBA 2Q96A 4FLJA 4FO8A 4QR8A 4R60A 2V6CA 1A16A 3TAVA 4S00A 4U73A 4U6WA 4KM3A 3BIQA 2P9AA 5CLSA 2Q95A 3PKAA 1R5GA 1WL6A 1YW8A 1WLRA 2GU7A 2GU6A 1CHMA 2OKNA 1C21A 4Z7MA 2Q93A 3OVKA 1XNZA 2Q92A 4U6ZA 2GG9A 4FKCA 1QXYA 2GG7A 2GZ5A 1YVMA 3FMRA 5CNXA 5CIKA 2BWTA 3PKCA 1C24A 4FLKA 1KQ0A 5FCFA 3BIPA 2EVCA 1Y1NA 5JI6A 2V3XA 1MATA 2GG8A 2GGCA 4U69A 3RORA 1WN1A 2BWSA 3L7GA 4S2TP 4IDYA 3OOOA 1XGSA 2IW2A 5JFRA
chains in the Genus database with same CATH superfamily
5E2CA 4U6JA 4U6CA 1XGNA 1C22A 2BWWA 1C23A 2B3HA 3FM3A 4A6VA 3BITA 3QOCA 4FLIA 4ZWOA 2GTXA 4IU6A 3Q6DA 4EGEA 4ZWPA 5D6FA 1M35A 2P98A 1KQ9A 2EA2A 4IPAA 1QXZA 2GU4A 3O5VA 2EVOA 2GU5A 1XGOA 3MATA 3PN9A 3RVAA 3PKEA 5E5BA 3CB6A 1R5HA 1QXWA 2ADUA 3IG4A 5D6EA 3PKBA 2BH3A 1BOAA 2BB7A 5FCHA 2BHDA 1XGMA 2G6PA 4JUQA 3IU8A 4FLLA 1YW7A 2GG3A 4ZWUA 3IU7A 2GG2A 4U6EA 2ZSGA 2GA2A 2OAZA 4PNCA 2BWVA 2DFIA 2BHBA 1YW9A 1BN5A 4U76A 2MATA 4A6WA 2BWUA 1B59A 5CDLA 3CTZA 2BHCA 1QZYA 3FMQA 4IKRA 1B6AA 2Q8KA 1R58A 4U75A 1WL9A 2P99A 1N51A 1WY2A 1YJ3A 1W2MA 2BN7A 2B3LA 2EVMA 5CDVA 5JHUA 2NQ6A 3TB5A 1WKMA 4IKUA 3PKDA 4U1BA 2BHAA 2GG5A 4PV4A 4HXXA 2B3KA 2BWYA 4MATA 5CDEA 3I7MA 3CB5A 4IKSA 1C27A 4RZZA 4RGZ1 2V3ZA 3IL0A 4U70A 2HOWA 4U71A 5CE6A 4S2RP 4IKTA 1WBQA 1JAWA 4B28A 3D27A 2GGBA 4FO7A 2GG0A 2Q94A 4ZNGA 3MR1A 4FUKA 4OOKA 3MX6A 2EA4A 1W7VA 4S01A 1PV9A 4IECA 4RZYA 2V3YA 2NQ7A 3S6BA 1KP0A 2BWXA 3L24A 3IU9A 1O0XA 4IF7A 3PEBA 2Q96A 4FLJA 4FO8A 4QR8A 4R60A 2V6CA 1A16A 3TAVA 4S00A 4U73A 4U6WA 4KM3A 3BIQA 2P9AA 5CLSA 2Q95A 3PKAA 1R5GA 1WL6A 1YW8A 1WLRA 2GU7A 2GU6A 1CHMA 2OKNA 1C21A 4Z7MA 2Q93A 3OVKA 1XNZA 2Q92A 4U6ZA 2GG9A 4FKCA 1QXYA 2GG7A 2GZ5A 1YVMA 3FMRA 5CNXA 5CIKA 2BWTA 3PKCA 1C24A 4FLKA 1KQ0A 5FCFA 3BIPA 2EVCA 1Y1NA 5JI6A 2V3XA 1MATA 2GG8A 2GGCA 4U69A 3RORA 1WN1A 2BWSA 3L7GA 4S2TP 4IDYA 3OOOA 1XGSA 2IW2A 5JFRA
chains in the Genus database with same CATH topology
5E2CA 4U6JA 4U6CA 1XGNA 1C22A 2BWWA 1C23A 2B3HA 3FM3A 4A6VA 3BITA 3QOCA 4FLIA 4ZWOA 2GTXA 4IU6A 3Q6DA 4EGEA 4ZWPA 5D6FA 1M35A 2P98A 1KQ9A 2EA2A 4IPAA 1QXZA 2GU4A 3O5VA 2EVOA 2GU5A 1XGOA 3MATA 3PN9A 3RVAA 3PKEA 5E5BA 3CB6A 1R5HA 1QXWA 2ADUA 3IG4A 5D6EA 3PKBA 2BH3A 1BOAA 2BB7A 5FCHA 2BHDA 1XGMA 2G6PA 4JUQA 3IU8A 4FLLA 1YW7A 2GG3A 4ZWUA 3IU7A 2GG2A 4U6EA 2ZSGA 2GA2A 2OAZA 4PNCA 2BWVA 2DFIA 2BHBA 1YW9A 1BN5A 4U76A 2MATA 4A6WA 2BWUA 1B59A 5CDLA 3CTZA 2BHCA 1QZYA 3FMQA 4IKRA 1B6AA 2Q8KA 1R58A 4U75A 1WL9A 2P99A 1N51A 1WY2A 1YJ3A 1W2MA 2BN7A 2B3LA 2EVMA 5CDVA 5JHUA 2NQ6A 3TB5A 1WKMA 4IKUA 3PKDA 4U1BA 2BHAA 2GG5A 4PV4A 4HXXA 2B3KA 2BWYA 4MATA 5CDEA 3I7MA 3CB5A 4IKSA 1C27A 4RZZA 4RGZ1 2V3ZA 3IL0A 4U70A 2HOWA 4U71A 5CE6A 4S2RP 4IKTA 1WBQA 1JAWA 4B28A 3D27A 2GGBA 4FO7A 2GG0A 2Q94A 4ZNGA 3MR1A 4FUKA 4OOKA 3MX6A 2EA4A 1W7VA 4S01A 1PV9A 4IECA 4RZYA 2V3YA 2NQ7A 3S6BA 1KP0A 2BWXA 3L24A 3IU9A 1O0XA 4IF7A 3PEBA 2Q96A 4FLJA 4FO8A 4QR8A 4R60A 2V6CA 1A16A 3TAVA 4S00A 4U73A 4U6WA 4KM3A 3BIQA 2P9AA 5CLSA 2Q95A 3PKAA 1R5GA 1WL6A 1YW8A 1WLRA 2GU7A 2GU6A 1CHMA 2OKNA 1C21A 4Z7MA 2Q93A 3OVKA 1XNZA 2Q92A 4U6ZA 2GG9A 4FKCA 1QXYA 2GG7A 2GZ5A 1YVMA 3FMRA 5CNXA 5CIKA 2BWTA 3PKCA 1C24A 4FLKA 1KQ0A 5FCFA 3BIPA 2EVCA 1Y1NA 5JI6A 2V3XA 1MATA 2GG8A 2GGCA 4U69A 3RORA 1WN1A 2BWSA 3L7GA 4S2TP 4IDYA 3OOOA 1XGSA 2IW2A 5JFRA
chains in the Genus database with same CATH homology


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