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


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