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


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