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.

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


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