4S00A

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp mutant y366a in complex with acrylate
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
RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKAGCLMHGVGLCDEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA
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 4s00A01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4s00A02
2EVMA 4IKSA 1C23A 3FMQA 1KQ9A 2B3LA 3MR1A 5CNXA 4ZNGA 4RGZ1 5D6EA 1MATA 4U6EA 1XGOA 1C27A 3PKBA 2BHDA 4IKUA 2BWSA 4RZYA 4FKCA 4U73A 1WY2A 2GA2A 5CDEA 4U76A 2HOWA 3L7GA 2BH3A 1JAWA 3BIQA 1YW7A 3RORA 4FO7A 1CHMA 2BHAA 2GG7A 1XGMA 1O0XA 1QXWA 5CDLA 2ZSGA 4U70A 3IU9A 2GGBA 5CDVA 2GZ5A 4U75A 4A6VA 2NQ7A 3PKDA 4IKRA 4S00A 2P99A 2Q8KA 2P98A 3MX6A 4IECA 2GG8A 4FLLA 2V3YA 2BWXA 3BITA 1BN5A 5JI6A 3CTZA 2B3HA 2BWYA 2EA2A 3CB6A 4ZWOA 1B59A 4ZWUA 1C21A 4FLJA 3Q6DA 4PNCA 4B28A 1KP0A 3BIPA 4R60A 5E2CA 2BB7A 2V6CA 1QXZA 3PKEA 4FO8A 1R58A 2Q96A 4OOKA 2GU5A 2BN7A 2BWWA 3S6BA 5CIKA 2Q95A 4RZZA 3FM3A 1WN1A 4PV4A 4U6WA 3IU7A 4QR8A 1R5GA 3FMRA 4JUQA 1B6AA 4MATA 1BOAA 2P9AA 4Z7MA 2BWUA 1C24A 1QZYA 2B3KA 2GG3A 2GG0A 4IF7A 2GU6A 4U71A 4EGEA 5CLSA 3OVKA 3PEBA 4U6CA 3TB5A 5FCHA 4IU6A 2GG2A 2V3ZA 4IKTA 4U1BA 3I7MA 1WLRA 2DFIA 1R5HA 3O5VA 1W2MA 2Q92A 1N51A 2G6PA 3IU8A 2EA4A 2NQ6A 2EVOA 2V3XA 1XGSA 1XNZA 1PV9A 3PKCA 4ZWPA 2GGCA 4U6JA 3TAVA 5JHUA 2EVCA 1W7VA 3PN9A 4FLIA 4FLKA 4FUKA 2GU7A 2OAZA 2BWVA 1M35A 2BHCA 3D27A 2GTXA 5E5BA 5FCFA 1YW9A 3CB5A 2MATA 4A6WA 1XGNA 5JFRA 2ADUA 2BHBA 4HXXA 1Y1NA 3L24A 2GG5A 3MATA 4U69A 3IL0A 2IW2A 1WKMA 1KQ0A 1WL6A 1A16A 1YJ3A 1WBQA 4IDYA 4S2RP 1YVMA 3OOOA 1C22A 1YW8A 4IPAA 4U6ZA 2Q93A 2GU4A 3PKAA 4S01A 2Q94A 5CE6A 3IG4A 2OKNA 1WL9A 2BWTA 3QOCA 4S2TP 2GG9A 5D6FA 1QXYA 4KM3A 3RVAA
chains in the Genus database with same CATH superfamily
2EVMA 4IKSA 1C23A 3FMQA 1KQ9A 2B3LA 3MR1A 5CNXA 4ZNGA 4RGZ1 5D6EA 1MATA 4U6EA 1XGOA 1C27A 3PKBA 2BHDA 4IKUA 2BWSA 4RZYA 4FKCA 4U73A 1WY2A 2GA2A 5CDEA 4U76A 2HOWA 3L7GA 2BH3A 1JAWA 3BIQA 1YW7A 3RORA 4FO7A 1CHMA 2BHAA 2GG7A 1XGMA 1O0XA 1QXWA 5CDLA 2ZSGA 4U70A 3IU9A 2GGBA 5CDVA 2GZ5A 4U75A 4A6VA 2NQ7A 3PKDA 4IKRA 4S00A 2P99A 2Q8KA 2P98A 3MX6A 4IECA 2GG8A 4FLLA 2V3YA 2BWXA 3BITA 1BN5A 5JI6A 3CTZA 2B3HA 2BWYA 2EA2A 3CB6A 4ZWOA 1B59A 4ZWUA 1C21A 4FLJA 3Q6DA 4PNCA 4B28A 1KP0A 3BIPA 4R60A 5E2CA 2BB7A 2V6CA 1QXZA 3PKEA 4FO8A 1R58A 2Q96A 4OOKA 2GU5A 2BN7A 2BWWA 3S6BA 5CIKA 2Q95A 4RZZA 3FM3A 1WN1A 4PV4A 4U6WA 3IU7A 4QR8A 1R5GA 3FMRA 4JUQA 1B6AA 4MATA 1BOAA 2P9AA 4Z7MA 2BWUA 1C24A 1QZYA 2B3KA 2GG3A 2GG0A 4IF7A 2GU6A 4U71A 4EGEA 5CLSA 3OVKA 3PEBA 4U6CA 3TB5A 5FCHA 4IU6A 2GG2A 2V3ZA 4IKTA 4U1BA 3I7MA 1WLRA 2DFIA 1R5HA 3O5VA 1W2MA 2Q92A 1N51A 2G6PA 3IU8A 2EA4A 2NQ6A 2EVOA 2V3XA 1XGSA 1XNZA 1PV9A 3PKCA 4ZWPA 2GGCA 4U6JA 3TAVA 5JHUA 2EVCA 1W7VA 3PN9A 4FLIA 4FLKA 4FUKA 2GU7A 2OAZA 2BWVA 1M35A 2BHCA 3D27A 2GTXA 5E5BA 5FCFA 1YW9A 3CB5A 2MATA 4A6WA 1XGNA 5JFRA 2ADUA 2BHBA 4HXXA 1Y1NA 3L24A 2GG5A 3MATA 4U69A 3IL0A 2IW2A 1WKMA 1KQ0A 1WL6A 1A16A 1YJ3A 1WBQA 4IDYA 4S2RP 1YVMA 3OOOA 1C22A 1YW8A 4IPAA 4U6ZA 2Q93A 2GU4A 3PKAA 4S01A 2Q94A 5CE6A 3IG4A 2OKNA 1WL9A 2BWTA 3QOCA 4S2TP 2GG9A 5D6FA 1QXYA 4KM3A 3RVAA
chains in the Genus database with same CATH topology
2EVMA 4IKSA 1C23A 3FMQA 1KQ9A 2B3LA 3MR1A 5CNXA 4ZNGA 4RGZ1 5D6EA 1MATA 4U6EA 1XGOA 1C27A 3PKBA 2BHDA 4IKUA 2BWSA 4RZYA 4FKCA 4U73A 1WY2A 2GA2A 5CDEA 4U76A 2HOWA 3L7GA 2BH3A 1JAWA 3BIQA 1YW7A 3RORA 4FO7A 1CHMA 2BHAA 2GG7A 1XGMA 1O0XA 1QXWA 5CDLA 2ZSGA 4U70A 3IU9A 2GGBA 5CDVA 2GZ5A 4U75A 4A6VA 2NQ7A 3PKDA 4IKRA 4S00A 2P99A 2Q8KA 2P98A 3MX6A 4IECA 2GG8A 4FLLA 2V3YA 2BWXA 3BITA 1BN5A 5JI6A 3CTZA 2B3HA 2BWYA 2EA2A 3CB6A 4ZWOA 1B59A 4ZWUA 1C21A 4FLJA 3Q6DA 4PNCA 4B28A 1KP0A 3BIPA 4R60A 5E2CA 2BB7A 2V6CA 1QXZA 3PKEA 4FO8A 1R58A 2Q96A 4OOKA 2GU5A 2BN7A 2BWWA 3S6BA 5CIKA 2Q95A 4RZZA 3FM3A 1WN1A 4PV4A 4U6WA 3IU7A 4QR8A 1R5GA 3FMRA 4JUQA 1B6AA 4MATA 1BOAA 2P9AA 4Z7MA 2BWUA 1C24A 1QZYA 2B3KA 2GG3A 2GG0A 4IF7A 2GU6A 4U71A 4EGEA 5CLSA 3OVKA 3PEBA 4U6CA 3TB5A 5FCHA 4IU6A 2GG2A 2V3ZA 4IKTA 4U1BA 3I7MA 1WLRA 2DFIA 1R5HA 3O5VA 1W2MA 2Q92A 1N51A 2G6PA 3IU8A 2EA4A 2NQ6A 2EVOA 2V3XA 1XGSA 1XNZA 1PV9A 3PKCA 4ZWPA 2GGCA 4U6JA 3TAVA 5JHUA 2EVCA 1W7VA 3PN9A 4FLIA 4FLKA 4FUKA 2GU7A 2OAZA 2BWVA 1M35A 2BHCA 3D27A 2GTXA 5E5BA 5FCFA 1YW9A 3CB5A 2MATA 4A6WA 1XGNA 5JFRA 2ADUA 2BHBA 4HXXA 1Y1NA 3L24A 2GG5A 3MATA 4U69A 3IL0A 2IW2A 1WKMA 1KQ0A 1WL6A 1A16A 1YJ3A 1WBQA 4IDYA 4S2RP 1YVMA 3OOOA 1C22A 1YW8A 4IPAA 4U6ZA 2Q93A 2GU4A 3PKAA 4S01A 2Q94A 5CE6A 3IG4A 2OKNA 1WL9A 2BWTA 3QOCA 4S2TP 2GG9A 5D6FA 1QXYA 4KM3A 3RVAA
chains in the Genus database with same CATH homology


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