4S01A

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (dmsp) lyase rldddp mutant d377n 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
RKIDPSRGATLGDGTPNDNDRIEIGPTQLAFSEWAAAGLQLPNLDRMREYRWKRLTQAIVDRGYGGLLMFDPLNIRYATDSTNMQLWNTHNPFRAVLLCADGYMVIWDYKNSPFLSKFNPLVREQRSGADLFYFDRGDKVDVQADVFANEVRVLMQDHAPGHTRLAVDKIMLHGLRALEAQGFEIMEGEEVTEKTRAIKGPDEILAMRCASHACETAVAEMEKFARAHVGDGKTSEDDIWAVLHAENIKRGGEWIETRLLASGPRTNPWFQECGPRITQKNEIIAFDTDLIGSYGICVDISRTWWIGDQKPRPDMVYAMQHAHEHIMTNMEMLKPGVMIPDLTANCHRLDDKFQAQKYGCLMHGVGLCNEWPLVAYPDKAVPGSYDYPLEPGMVLCVEAAVGEVGGDFSIKLEDQVLITEDGYENLTTYPFDAALMGLA
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 4s01A01
3.90.230.10 Alpha Beta Alpha-Beta Complex Creatine Amidinohydrolase Creatinase/methionine aminopeptidase superfamily 4s01A02
1BOAA 3CB5A 1YW9A 2P9AA 3FMQA 1M35A 4RZYA 1W2MA 4QR8A 4S2TP 1CHMA 1QXWA 4U75A 4U6WA 2B3LA 4S2RP 2ADUA 5CDEA 4IDYA 4U76A 4IECA 4ZNGA 2BB7A 1QXYA 4IF7A 2GTXA 4U6CA 3PN9A 2HOWA 3FM3A 2OAZA 3TAVA 1KQ0A 4ZWOA 3BITA 4FUKA 2V3YA 4U70A 2Q8KA 3S6BA 5E2CA 4RZZA 1YW7A 2BN7A 3MATA 2BWYA 1MATA 2GU6A 2EVMA 2GZ5A 3FMRA 1WL6A 1R5HA 4U1BA 3PKDA 1WBQA 5CDLA 2BWXA 1YVMA 2Q96A 1W7VA 1KQ9A 5CIKA 2BHCA 5JFRA 1JAWA 1A16A 1QZYA 4MATA 2V3XA 5FCFA 2BHAA 4A6WA 1C22A 3QOCA 4IPAA 4OOKA 2P99A 3RORA 5JHUA 1C21A 2GGCA 4ZWPA 4FLKA 3L24A 2GU5A 1WKMA 1XGOA 4PV4A 1O0XA 3TB5A 1N51A 2GG3A 4S00A 4IKRA 3OOOA 4S01A 1KP0A 1Y1NA 2BWSA 4U6ZA 3PKBA 2IW2A 2GG7A 2MATA 4IKUA 4IU6A 5CE6A 4KM3A 4U73A 3PEBA 1XGSA 4HXXA 3PKCA 5D6EA 1YJ3A 2BWWA 3L7GA 4U6JA 4A6VA 3PKAA 4U69A 5CNXA 1XGMA 2NQ6A 2DFIA 2Q95A 1WLRA 2GU4A 1WY2A 3O5VA 1PV9A 5E5BA 4FO8A 1C27A 2GG8A 4FLJA 2GGBA 2EA4A 1XGNA 3I7MA 4B28A 3D27A 4IKSA 3RVAA 3IU7A 2OKNA 2G6PA 3IU8A 3IL0A 3CB6A 1QXZA 4U71A 2BHBA 2BHDA 4IKTA 5CDVA 1WL9A 3PKEA 1R58A 2NQ7A 4FO7A 3MR1A 2ZSGA 1B6AA 3BIQA 1C23A 5JI6A 4PNCA 2P98A 3MX6A 2BWTA 2BH3A 2Q94A 2GA2A 2EVOA 2EA2A 4R60A 3OVKA 5D6FA 4ZWUA 5FCHA 1BN5A 2GG0A 3BIPA 1B59A 4Z7MA 1C24A 2GU7A 2BWVA 5CLSA 4FKCA 4RGZ1 4FLLA 2V3ZA 2V6CA 4EGEA 4JUQA 1WN1A 3CTZA 2GG5A 1R5GA 2BWUA 2GG9A 2Q92A 1XNZA 2EVCA 2B3KA 2B3HA 3Q6DA 3IU9A 2GG2A 3IG4A 4U6EA 1YW8A 4FLIA 2Q93A
chains in the Genus database with same CATH superfamily
1BOAA 3CB5A 1YW9A 2P9AA 3FMQA 1M35A 4RZYA 1W2MA 4QR8A 4S2TP 1CHMA 1QXWA 4U75A 4U6WA 2B3LA 4S2RP 2ADUA 5CDEA 4IDYA 4U76A 4IECA 4ZNGA 2BB7A 1QXYA 4IF7A 2GTXA 4U6CA 3PN9A 2HOWA 3FM3A 2OAZA 3TAVA 1KQ0A 4ZWOA 3BITA 4FUKA 2V3YA 4U70A 2Q8KA 3S6BA 5E2CA 4RZZA 1YW7A 2BN7A 3MATA 2BWYA 1MATA 2GU6A 2EVMA 2GZ5A 3FMRA 1WL6A 1R5HA 4U1BA 3PKDA 1WBQA 5CDLA 2BWXA 1YVMA 2Q96A 1W7VA 1KQ9A 5CIKA 2BHCA 5JFRA 1JAWA 1A16A 1QZYA 4MATA 2V3XA 5FCFA 2BHAA 4A6WA 1C22A 3QOCA 4IPAA 4OOKA 2P99A 3RORA 5JHUA 1C21A 2GGCA 4ZWPA 4FLKA 3L24A 2GU5A 1WKMA 1XGOA 4PV4A 1O0XA 3TB5A 1N51A 2GG3A 4S00A 4IKRA 3OOOA 4S01A 1KP0A 1Y1NA 2BWSA 4U6ZA 3PKBA 2IW2A 2GG7A 2MATA 4IKUA 4IU6A 5CE6A 4KM3A 4U73A 3PEBA 1XGSA 4HXXA 3PKCA 5D6EA 1YJ3A 2BWWA 3L7GA 4U6JA 4A6VA 3PKAA 4U69A 5CNXA 1XGMA 2NQ6A 2DFIA 2Q95A 1WLRA 2GU4A 1WY2A 3O5VA 1PV9A 5E5BA 4FO8A 1C27A 2GG8A 4FLJA 2GGBA 2EA4A 1XGNA 3I7MA 4B28A 3D27A 4IKSA 3RVAA 3IU7A 2OKNA 2G6PA 3IU8A 3IL0A 3CB6A 1QXZA 4U71A 2BHBA 2BHDA 4IKTA 5CDVA 1WL9A 3PKEA 1R58A 2NQ7A 4FO7A 3MR1A 2ZSGA 1B6AA 3BIQA 1C23A 5JI6A 4PNCA 2P98A 3MX6A 2BWTA 2BH3A 2Q94A 2GA2A 2EVOA 2EA2A 4R60A 3OVKA 5D6FA 4ZWUA 5FCHA 1BN5A 2GG0A 3BIPA 1B59A 4Z7MA 1C24A 2GU7A 2BWVA 5CLSA 4FKCA 4RGZ1 4FLLA 2V3ZA 2V6CA 4EGEA 4JUQA 1WN1A 3CTZA 2GG5A 1R5GA 2BWUA 2GG9A 2Q92A 1XNZA 2EVCA 2B3KA 2B3HA 3Q6DA 3IU9A 2GG2A 3IG4A 4U6EA 1YW8A 4FLIA 2Q93A
chains in the Genus database with same CATH topology
1BOAA 3CB5A 1YW9A 2P9AA 3FMQA 1M35A 4RZYA 1W2MA 4QR8A 4S2TP 1CHMA 1QXWA 4U75A 4U6WA 2B3LA 4S2RP 2ADUA 5CDEA 4IDYA 4U76A 4IECA 4ZNGA 2BB7A 1QXYA 4IF7A 2GTXA 4U6CA 3PN9A 2HOWA 3FM3A 2OAZA 3TAVA 1KQ0A 4ZWOA 3BITA 4FUKA 2V3YA 4U70A 2Q8KA 3S6BA 5E2CA 4RZZA 1YW7A 2BN7A 3MATA 2BWYA 1MATA 2GU6A 2EVMA 2GZ5A 3FMRA 1WL6A 1R5HA 4U1BA 3PKDA 1WBQA 5CDLA 2BWXA 1YVMA 2Q96A 1W7VA 1KQ9A 5CIKA 2BHCA 5JFRA 1JAWA 1A16A 1QZYA 4MATA 2V3XA 5FCFA 2BHAA 4A6WA 1C22A 3QOCA 4IPAA 4OOKA 2P99A 3RORA 5JHUA 1C21A 2GGCA 4ZWPA 4FLKA 3L24A 2GU5A 1WKMA 1XGOA 4PV4A 1O0XA 3TB5A 1N51A 2GG3A 4S00A 4IKRA 3OOOA 4S01A 1KP0A 1Y1NA 2BWSA 4U6ZA 3PKBA 2IW2A 2GG7A 2MATA 4IKUA 4IU6A 5CE6A 4KM3A 4U73A 3PEBA 1XGSA 4HXXA 3PKCA 5D6EA 1YJ3A 2BWWA 3L7GA 4U6JA 4A6VA 3PKAA 4U69A 5CNXA 1XGMA 2NQ6A 2DFIA 2Q95A 1WLRA 2GU4A 1WY2A 3O5VA 1PV9A 5E5BA 4FO8A 1C27A 2GG8A 4FLJA 2GGBA 2EA4A 1XGNA 3I7MA 4B28A 3D27A 4IKSA 3RVAA 3IU7A 2OKNA 2G6PA 3IU8A 3IL0A 3CB6A 1QXZA 4U71A 2BHBA 2BHDA 4IKTA 5CDVA 1WL9A 3PKEA 1R58A 2NQ7A 4FO7A 3MR1A 2ZSGA 1B6AA 3BIQA 1C23A 5JI6A 4PNCA 2P98A 3MX6A 2BWTA 2BH3A 2Q94A 2GA2A 2EVOA 2EA2A 4R60A 3OVKA 5D6FA 4ZWUA 5FCHA 1BN5A 2GG0A 3BIPA 1B59A 4Z7MA 1C24A 2GU7A 2BWVA 5CLSA 4FKCA 4RGZ1 4FLLA 2V3ZA 2V6CA 4EGEA 4JUQA 1WN1A 3CTZA 2GG5A 1R5GA 2BWUA 2GG9A 2Q92A 1XNZA 2EVCA 2B3KA 2B3HA 3Q6DA 3IU9A 2GG2A 3IG4A 4U6EA 1YW8A 4FLIA 2Q93A
chains in the Genus database with same CATH homology


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