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


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