4RZZA

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp in complex with phosphate
Total Genus 158
50100150200250300350400020406080100120140160
Genus TraceResidueGenus

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
50100150200250300350400400300200100
050100150Genus Matrix

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
source organism Silicibacter lacuscaerulensis iti-1157
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
molecule keywords Peptidase M24
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
3BITA 5CLSA 4IKUA 1XGNA 2G6PA 2HOWA 2ZSGA 1WBQA 2GG9A 2V3YA 2NQ7A 3IU7A 4RZYA 1C24A 2GGCA 1W2MA 5FCFA 1BOAA 3BIQA 2Q8KA 2GU4A 4U6JA 2EVCA 1R58A 3IU8A 4PNCA 2V3ZA 4U70A 4FLJA 4IF7A 1B59A 3FMQA 3MR1A 2OAZA 4MATA 2BHDA 3PEBA 1XGOA 3CB6A 1R5GA 3PKCA 2GU6A 2BHAA 4S2RP 5D6EA 1QXWA 1O0XA 2P9AA 2BHBA 3PKEA 3CB5A 2Q94A 4IECA 5E5BA 3BIPA 2GG2A 2GG7A 5JI6A 1KQ9A 1W7VA 1N51A 5CDLA 4FO7A 2Q95A 1WLRA 1CHMA 2BWYA 3IG4A 1B6AA 2MATA 2BN7A 3L7GA 3MATA 4IKTA 3O5VA 4A6WA 1XGSA 4ZNGA 1Y1NA 4FLKA 1PV9A 3I7MA 1C22A 4ZWPA 1C21A 3PKBA 3QOCA 1WKMA 2BH3A 2GG3A 2IW2A 5E2CA 2DFIA 4U75A 3IL0A 4S01A 1YW9A 2B3LA 2GG5A 3OVKA 1JAWA 1KQ0A 3S6BA 2BHCA 3TB5A 2V3XA 2BWSA 2GG8A 4IU6A 4U6CA 3D27A 2Q96A 4FLLA 4Z7MA 2EA4A 4FUKA 4U6ZA 2GZ5A 2NQ6A 1MATA 1R5HA 4PV4A 5JFRA 2B3KA 4U6EA 5FCHA 4ZWOA 2BWWA 3PKAA 4IKSA 3CTZA 1YW8A 1YVMA 2BWVA 4HXXA 2BWTA 5CIKA 2Q92A 2ADUA 5CDEA 2Q93A 5CNXA 1QZYA 4B28A 1WL9A 3IU9A 4QR8A 4RZZA 2GG0A 2V6CA 2P98A 4OOKA 4U1BA 1YJ3A 3PN9A 3TAVA 3MX6A 4EGEA 2EVMA 4IKRA 2BB7A 4S00A 3FMRA 4A6VA 1XGMA 2BWUA 1C23A 4IPAA 1WL6A 3Q6DA 4U76A 1KP0A 1WY2A 3L24A 4JUQA 4FO8A 1XNZA 4KM3A 1YW7A 4FKCA 2BWXA 4U6WA 5CE6A 4U71A 4U69A 3OOOA 4R60A 4U73A 1M35A 2GU7A 4RGZ1 5D6FA 5JHUA 2B3HA 3RORA 1QXYA 2GU5A 4IDYA 3PKDA 4ZWUA 2GA2A 4FLIA 1WN1A 1A16A 5CDVA 2EVOA 3RVAA 2P99A 2OKNA 1BN5A 3FM3A 1C27A 2EA2A 2GGBA 1QXZA 4S2TP 2GTXA
chains in the Genus database with same CATH superfamily
3BITA 5CLSA 4IKUA 1XGNA 2G6PA 2HOWA 2ZSGA 1WBQA 2GG9A 2V3YA 2NQ7A 3IU7A 4RZYA 1C24A 2GGCA 1W2MA 5FCFA 1BOAA 3BIQA 2Q8KA 2GU4A 4U6JA 2EVCA 1R58A 3IU8A 4PNCA 2V3ZA 4U70A 4FLJA 4IF7A 1B59A 3FMQA 3MR1A 2OAZA 4MATA 2BHDA 3PEBA 1XGOA 3CB6A 1R5GA 3PKCA 2GU6A 2BHAA 4S2RP 5D6EA 1QXWA 1O0XA 2P9AA 2BHBA 3PKEA 3CB5A 2Q94A 4IECA 5E5BA 3BIPA 2GG2A 2GG7A 5JI6A 1KQ9A 1W7VA 1N51A 5CDLA 4FO7A 2Q95A 1WLRA 1CHMA 2BWYA 3IG4A 1B6AA 2MATA 2BN7A 3L7GA 3MATA 4IKTA 3O5VA 4A6WA 1XGSA 4ZNGA 1Y1NA 4FLKA 1PV9A 3I7MA 1C22A 4ZWPA 1C21A 3PKBA 3QOCA 1WKMA 2BH3A 2GG3A 2IW2A 5E2CA 2DFIA 4U75A 3IL0A 4S01A 1YW9A 2B3LA 2GG5A 3OVKA 1JAWA 1KQ0A 3S6BA 2BHCA 3TB5A 2V3XA 2BWSA 2GG8A 4IU6A 4U6CA 3D27A 2Q96A 4FLLA 4Z7MA 2EA4A 4FUKA 4U6ZA 2GZ5A 2NQ6A 1MATA 1R5HA 4PV4A 5JFRA 2B3KA 4U6EA 5FCHA 4ZWOA 2BWWA 3PKAA 4IKSA 3CTZA 1YW8A 1YVMA 2BWVA 4HXXA 2BWTA 5CIKA 2Q92A 2ADUA 5CDEA 2Q93A 5CNXA 1QZYA 4B28A 1WL9A 3IU9A 4QR8A 4RZZA 2GG0A 2V6CA 2P98A 4OOKA 4U1BA 1YJ3A 3PN9A 3TAVA 3MX6A 4EGEA 2EVMA 4IKRA 2BB7A 4S00A 3FMRA 4A6VA 1XGMA 2BWUA 1C23A 4IPAA 1WL6A 3Q6DA 4U76A 1KP0A 1WY2A 3L24A 4JUQA 4FO8A 1XNZA 4KM3A 1YW7A 4FKCA 2BWXA 4U6WA 5CE6A 4U71A 4U69A 3OOOA 4R60A 4U73A 1M35A 2GU7A 4RGZ1 5D6FA 5JHUA 2B3HA 3RORA 1QXYA 2GU5A 4IDYA 3PKDA 4ZWUA 2GA2A 4FLIA 1WN1A 1A16A 5CDVA 2EVOA 3RVAA 2P99A 2OKNA 1BN5A 3FM3A 1C27A 2EA2A 2GGBA 1QXZA 4S2TP 2GTXA
chains in the Genus database with same CATH topology
3BITA 5CLSA 4IKUA 1XGNA 2G6PA 2HOWA 2ZSGA 1WBQA 2GG9A 2V3YA 2NQ7A 3IU7A 4RZYA 1C24A 2GGCA 1W2MA 5FCFA 1BOAA 3BIQA 2Q8KA 2GU4A 4U6JA 2EVCA 1R58A 3IU8A 4PNCA 2V3ZA 4U70A 4FLJA 4IF7A 1B59A 3FMQA 3MR1A 2OAZA 4MATA 2BHDA 3PEBA 1XGOA 3CB6A 1R5GA 3PKCA 2GU6A 2BHAA 4S2RP 5D6EA 1QXWA 1O0XA 2P9AA 2BHBA 3PKEA 3CB5A 2Q94A 4IECA 5E5BA 3BIPA 2GG2A 2GG7A 5JI6A 1KQ9A 1W7VA 1N51A 5CDLA 4FO7A 2Q95A 1WLRA 1CHMA 2BWYA 3IG4A 1B6AA 2MATA 2BN7A 3L7GA 3MATA 4IKTA 3O5VA 4A6WA 1XGSA 4ZNGA 1Y1NA 4FLKA 1PV9A 3I7MA 1C22A 4ZWPA 1C21A 3PKBA 3QOCA 1WKMA 2BH3A 2GG3A 2IW2A 5E2CA 2DFIA 4U75A 3IL0A 4S01A 1YW9A 2B3LA 2GG5A 3OVKA 1JAWA 1KQ0A 3S6BA 2BHCA 3TB5A 2V3XA 2BWSA 2GG8A 4IU6A 4U6CA 3D27A 2Q96A 4FLLA 4Z7MA 2EA4A 4FUKA 4U6ZA 2GZ5A 2NQ6A 1MATA 1R5HA 4PV4A 5JFRA 2B3KA 4U6EA 5FCHA 4ZWOA 2BWWA 3PKAA 4IKSA 3CTZA 1YW8A 1YVMA 2BWVA 4HXXA 2BWTA 5CIKA 2Q92A 2ADUA 5CDEA 2Q93A 5CNXA 1QZYA 4B28A 1WL9A 3IU9A 4QR8A 4RZZA 2GG0A 2V6CA 2P98A 4OOKA 4U1BA 1YJ3A 3PN9A 3TAVA 3MX6A 4EGEA 2EVMA 4IKRA 2BB7A 4S00A 3FMRA 4A6VA 1XGMA 2BWUA 1C23A 4IPAA 1WL6A 3Q6DA 4U76A 1KP0A 1WY2A 3L24A 4JUQA 4FO8A 1XNZA 4KM3A 1YW7A 4FKCA 2BWXA 4U6WA 5CE6A 4U71A 4U69A 3OOOA 4R60A 4U73A 1M35A 2GU7A 4RGZ1 5D6FA 5JHUA 2B3HA 3RORA 1QXYA 2GU5A 4IDYA 3PKDA 4ZWUA 2GA2A 4FLIA 1WN1A 1A16A 5CDVA 2EVOA 3RVAA 2P99A 2OKNA 1BN5A 3FM3A 1C27A 2EA2A 2GGBA 1QXZA 4S2TP 2GTXA
chains in the Genus database with same CATH homology


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