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.

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


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