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


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