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


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