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


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