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.

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


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