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.

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


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