4RZZA

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp in complex with phosphate
Total Genus 158
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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
158
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 tags Lyase
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 iti-1157
total genus 158
structure length 439
sequence length 439
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2014-12-27

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 4rzzA01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4rzzA02
2DFIA 2ADUA 2GGCA 1WN1A 1JAWA 2V3YA 2GG9A 1N51A 2GG3A 4FLLA 5D6FA 3I7MA 3S6BA 4QR8A 4U6CA 4R60A 2EVCA 1YW7A 2BWUA 5CIKA 1QXYA 2BHBA 4HXXA 4IECA 1BN5A 2GGBA 1C22A 4ZNGA 4EGEA 2GU5A 1MATA 1W2MA 4S01A 2Q8KA 2BWYA 4IKSA 2BHDA 1XGOA 1QXZA 3TAVA 2NQ7A 4RGZ1 5CDLA 3D27A 3CTZA 5E2CA 2GG0A 4IPAA 3IL0A 2BWWA 3BITA 2GG8A 2OKNA 2P9AA 4IDYA 1QXWA 1R58A 2NQ6A 3PKBA 4IKUA 1WBQA 4U6ZA 4U69A 3FMRA 1BOAA 1W7VA 4B28A 4MATA 5CLSA 3CB6A 3OOOA 4KM3A 5CDEA 2B3HA 2GA2A 3BIQA 4U70A 2Q92A 4U6JA 2BN7A 3TB5A 1WL9A 2Q93A 2GU6A 3RORA 4PNCA 2BWVA 4U6WA 1WY2A 1XGMA 2EA4A 4ZWUA 4S2TP 1XGSA 1CHMA 2B3KA 2BHCA 4FLIA 1YW8A 1WL6A 4FKCA 4A6WA 2Q95A 5D6EA 2Q94A 5CDVA 1B6AA 3PKDA 4FLJA 2Q96A 4ZWPA 2GZ5A 4OOKA 2P99A 1PV9A 3RVAA 1C27A 1WLRA 2GG7A 2GU4A 1XGNA 4RZYA 1C24A 2GU7A 1R5HA 1YVMA 2GTXA 2BWTA 4IKRA 1A16A 5E5BA 2BHAA 3L24A 4JUQA 1Y1NA 3MR1A 2ZSGA 3L7GA 4RZZA 2BWSA 2EVMA 4FUKA 3IG4A 1KQ9A 3MX6A 3FMQA 1KP0A 2EVOA 2GG5A 2BH3A 3IU8A 3CB5A 3Q6DA 3QOCA 4Z7MA 2V6CA 2V3XA 4U73A 2B3LA 4A6VA 5JHUA 3IU7A 1C21A 3IU9A 5FCFA 4S2RP 1R5GA 1B59A 1WKMA 3OVKA 4FO8A 3PN9A 2GG2A 3PEBA 1YW9A 4PV4A 2OAZA 3O5VA 2IW2A 1C23A 2EA2A 4S00A 2BB7A 5CE6A 1O0XA 1KQ0A 1QZYA 1XNZA 2P98A 3MATA 1M35A 4U6EA 4U75A 4U71A 5JI6A 2BWXA 5FCHA 4FO7A 5CNXA 1YJ3A 3FM3A 2HOWA 5JFRA 3BIPA 2MATA 3PKEA 4IU6A 3PKCA 3PKAA 4U76A 2V3ZA 2G6PA 4ZWOA 4IKTA 4FLKA 4U1BA 4IF7A
chains in the Genus database with same CATH superfamily
2DFIA 2ADUA 2GGCA 1WN1A 1JAWA 2V3YA 2GG9A 1N51A 2GG3A 4FLLA 5D6FA 3I7MA 3S6BA 4QR8A 4U6CA 4R60A 2EVCA 1YW7A 2BWUA 5CIKA 1QXYA 2BHBA 4HXXA 4IECA 1BN5A 2GGBA 1C22A 4ZNGA 4EGEA 2GU5A 1MATA 1W2MA 4S01A 2Q8KA 2BWYA 4IKSA 2BHDA 1XGOA 1QXZA 3TAVA 2NQ7A 4RGZ1 5CDLA 3D27A 3CTZA 5E2CA 2GG0A 4IPAA 3IL0A 2BWWA 3BITA 2GG8A 2OKNA 2P9AA 4IDYA 1QXWA 1R58A 2NQ6A 3PKBA 4IKUA 1WBQA 4U6ZA 4U69A 3FMRA 1BOAA 1W7VA 4B28A 4MATA 5CLSA 3CB6A 3OOOA 4KM3A 5CDEA 2B3HA 2GA2A 3BIQA 4U70A 2Q92A 4U6JA 2BN7A 3TB5A 1WL9A 2Q93A 2GU6A 3RORA 4PNCA 2BWVA 4U6WA 1WY2A 1XGMA 2EA4A 4ZWUA 4S2TP 1XGSA 1CHMA 2B3KA 2BHCA 4FLIA 1YW8A 1WL6A 4FKCA 4A6WA 2Q95A 5D6EA 2Q94A 5CDVA 1B6AA 3PKDA 4FLJA 2Q96A 4ZWPA 2GZ5A 4OOKA 2P99A 1PV9A 3RVAA 1C27A 1WLRA 2GG7A 2GU4A 1XGNA 4RZYA 1C24A 2GU7A 1R5HA 1YVMA 2GTXA 2BWTA 4IKRA 1A16A 5E5BA 2BHAA 3L24A 4JUQA 1Y1NA 3MR1A 2ZSGA 3L7GA 4RZZA 2BWSA 2EVMA 4FUKA 3IG4A 1KQ9A 3MX6A 3FMQA 1KP0A 2EVOA 2GG5A 2BH3A 3IU8A 3CB5A 3Q6DA 3QOCA 4Z7MA 2V6CA 2V3XA 4U73A 2B3LA 4A6VA 5JHUA 3IU7A 1C21A 3IU9A 5FCFA 4S2RP 1R5GA 1B59A 1WKMA 3OVKA 4FO8A 3PN9A 2GG2A 3PEBA 1YW9A 4PV4A 2OAZA 3O5VA 2IW2A 1C23A 2EA2A 4S00A 2BB7A 5CE6A 1O0XA 1KQ0A 1QZYA 1XNZA 2P98A 3MATA 1M35A 4U6EA 4U75A 4U71A 5JI6A 2BWXA 5FCHA 4FO7A 5CNXA 1YJ3A 3FM3A 2HOWA 5JFRA 3BIPA 2MATA 3PKEA 4IU6A 3PKCA 3PKAA 4U76A 2V3ZA 2G6PA 4ZWOA 4IKTA 4FLKA 4U1BA 4IF7A
chains in the Genus database with same CATH topology
2DFIA 2ADUA 2GGCA 1WN1A 1JAWA 2V3YA 2GG9A 1N51A 2GG3A 4FLLA 5D6FA 3I7MA 3S6BA 4QR8A 4U6CA 4R60A 2EVCA 1YW7A 2BWUA 5CIKA 1QXYA 2BHBA 4HXXA 4IECA 1BN5A 2GGBA 1C22A 4ZNGA 4EGEA 2GU5A 1MATA 1W2MA 4S01A 2Q8KA 2BWYA 4IKSA 2BHDA 1XGOA 1QXZA 3TAVA 2NQ7A 4RGZ1 5CDLA 3D27A 3CTZA 5E2CA 2GG0A 4IPAA 3IL0A 2BWWA 3BITA 2GG8A 2OKNA 2P9AA 4IDYA 1QXWA 1R58A 2NQ6A 3PKBA 4IKUA 1WBQA 4U6ZA 4U69A 3FMRA 1BOAA 1W7VA 4B28A 4MATA 5CLSA 3CB6A 3OOOA 4KM3A 5CDEA 2B3HA 2GA2A 3BIQA 4U70A 2Q92A 4U6JA 2BN7A 3TB5A 1WL9A 2Q93A 2GU6A 3RORA 4PNCA 2BWVA 4U6WA 1WY2A 1XGMA 2EA4A 4ZWUA 4S2TP 1XGSA 1CHMA 2B3KA 2BHCA 4FLIA 1YW8A 1WL6A 4FKCA 4A6WA 2Q95A 5D6EA 2Q94A 5CDVA 1B6AA 3PKDA 4FLJA 2Q96A 4ZWPA 2GZ5A 4OOKA 2P99A 1PV9A 3RVAA 1C27A 1WLRA 2GG7A 2GU4A 1XGNA 4RZYA 1C24A 2GU7A 1R5HA 1YVMA 2GTXA 2BWTA 4IKRA 1A16A 5E5BA 2BHAA 3L24A 4JUQA 1Y1NA 3MR1A 2ZSGA 3L7GA 4RZZA 2BWSA 2EVMA 4FUKA 3IG4A 1KQ9A 3MX6A 3FMQA 1KP0A 2EVOA 2GG5A 2BH3A 3IU8A 3CB5A 3Q6DA 3QOCA 4Z7MA 2V6CA 2V3XA 4U73A 2B3LA 4A6VA 5JHUA 3IU7A 1C21A 3IU9A 5FCFA 4S2RP 1R5GA 1B59A 1WKMA 3OVKA 4FO8A 3PN9A 2GG2A 3PEBA 1YW9A 4PV4A 2OAZA 3O5VA 2IW2A 1C23A 2EA2A 4S00A 2BB7A 5CE6A 1O0XA 1KQ0A 1QZYA 1XNZA 2P98A 3MATA 1M35A 4U6EA 4U75A 4U71A 5JI6A 2BWXA 5FCHA 4FO7A 5CNXA 1YJ3A 3FM3A 2HOWA 5JFRA 3BIPA 2MATA 3PKEA 4IU6A 3PKCA 3PKAA 4U76A 2V3ZA 2G6PA 4ZWOA 4IKTA 4FLKA 4U1BA 4IF7A
chains in the Genus database with same CATH homology


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