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.

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


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