1YCLA

Crystal structure of b. subtilis luxs in complex with a catalytic 2-ketone intermediate
Total Genus 44
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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
44
sequence length
154
structure length
154
Chain Sequence
VESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNKQAMKPDTIHTLEHLLAFTIRSHAEKYDHFDIIDISPMGAQTGYYLVVSGEPTSAEIVDLLEDTMKEAVEITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKEELLKVFG
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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.

Chord Diagram
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publication title Crystal Structure of S-Ribosylhomocysteinase (LuxS) in Complex with a Catalytic 2-Ketone Intermediate.
pubmed doi rcsb
source organism Bacillus subtilis
molecule tags Hydrolase
molecule keywords S-ribosylhomocysteinase
total genus 44
structure length 154
sequence length 154
ec nomenclature ec 4.4.1.21: S-ribosylhomocysteine lyase.
pdb deposition date 2004-12-22

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02664 LuxS S-Ribosylhomocysteinase (LuxS)
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.1360.80 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2 S-ribosylhomocysteinase (LuxS) 1yclA00
1J6VA 1INNA 1JQWA 1YCLA 1VH2A 1J6XA 1VGXA 2FQOA 1VJEA 2FQTA 1J6WA 1JOEA 4XCHA 1JVIA 5E68A 1J98A 1IE0A
chains in the Genus database with same CATH superfamily
3S1QK 3TTGA 4BBRK 3HOZC 4LLGA 4G0WA 3OPFA 4BLAA 3GTJA 4AYBD 2KWAA 4AH6A 3AD7C 3HOXC 5TMCA 1I50C 1TWFA 2YU9A 2WB1D 3M3YC 5M5XK 3AQPA 1ZVUA 5IORA 4A3IC 3GDZA 1RU0A 3S1RK 1BDFA 1J98A 1WSRA 2JH3A 3GTQC 2Y0SL 3BUEA 3L4JA 1B4AA 4QIWL 4C3IK 2PA8L 4GZYA 2CW0A 4A3LC 3AQOA 3S2HK 4BXXK 1X31C 3GTMA 1IE0A 4KB4A 1YCLA 2R92C 4A3MC 1DCPA 1XZPA 4GT9A 1J6XA 4FM9A 3S14C 3GTPA 2GSNA 3GTGA 3S1QC 1J6WA 1EQRA 5M3FK 3HOUC 4A3LK 5IYBK 4Q4ZA 3HKZL 2E2IK 3HOWC 1Y1VC 3I4MC 3CQZC 1TWAK 4Y52C 1TWHK 4A3DK 3BP3A 3T01A 2P5MA 4A3MK 4BBSK 1O27A 1B4BA 4GTCA 4C2MC 1Y1WA 2NVYC 4YFXA 1HI9A 3HOYC 2WAQD 3S17C 3HOXK 5IP9K 1WOOA 1IL2A 5IYDK 1O25A 4BY1K 2W7VA 1AB4A 3MMLB 2B63A 5C3EK 5HL8A 3GTOA 1TWHA 4KARA 1ZYRA 2Y3PA 4P5BA 2RGRA 1IBAA 3OEPA 1YNJA 3S16C 1TWGA 3AD8C 4C45A 3S1NK 3GEIA 2A6HA 1IW7A 2A68A 2ZUFA 3N3YA 1USOA 4XSXA 4G7OA 1I3QC 3M4OK 4A93C 3I4MK 2O5IA 5IP9C 4GTBA 4A3CC 2JA6A 2PHCB 1O2FB 3GTJK 2NVYK 4GTDA 3T02A 4YFKA 1I6VA 4GTFA 2YU9C 1O2BA 4YG2A 4KN7A 1EH1A 3M4OC 4ZH4A 3RZOK 4LQYA 1VRQC 2JA8K 3HKZD 2R7ZK 3GTQA 1O24A 2JA5K 3S2DC 3VA7A 2V6UA 5C44K 1I50A 1ZXOA 4A3JK 1XXCA 3OREA 4G0VA 2R92A 3PO3C 4MEYA 2CFAB 3GTMC 1G51A 3GTPK 1I3QK 1WOSA 3S15C 4GTLA 1USMA 3N0CA 2ZUEA 5FLMK 3GTGC 1WQHA 3TFIA 5E68A 1R9TK 1TWAA 4KMHA 3NUHA 5FLMC 1I6HC 2XCOA 4BBSC 1XZPB 2E2HA 4QJVA 4KC6A 3CQZK 3HOVK 4A3GK 1WQFA 4BBRC 3H3VD 1XZQB 5IOTA 3DXJA 1INNA 2JA7K 3LPXA 1WCMK 5D4DA 3QX3A 3S2DK 4GTAA 3A8IA 3FKIC 4KN4A 1WSVA 4M1XA 4OIQA 4X6AK 2YU9K 2O5JA 2E2HK 3GSIA 1JOEA 1F9NA 1C0AA 2XCQA 3GTKC 3SZZA 2GSOA 1VJEA 5C4XC 2JA7C 3HOUK 2JA5A 5M3MK 3FKIA 1HQMA 3N0BA 3PO2C 4BKWA 4C3IC 1R9TC 4A93K 1GE9A 3ERED 4WILA 3H0GK 1UV7A 3T00A 1BS2A 2R92K 1KQ4A 5IOSA 5IP7K 3GEHA 1TWCK 1EFWA 3S1NC 4AYBL 1BJTA 1XZQA 1PJ5A 3BP8C 2R7ZA 2R93C 1I50K 2VUMK 2GAHC 5JFEA 3K7AK 1VGXA 1DCOA 3PO2K 5IP7C 3GTQK 4LK1A 4LOWA 3S15K 2V6SA 3H0GC 4MQ9A 3M3YK 2JA6C 5IYDC 3ADAC 3HXAA 2PA8D 3A8KA 2VUMC 1DCHA 1O28A 4RMFA 1VLOA 3JSTA 1O26A 4C2MK 1F93A 2B63K 5C44C 3GTKK 4KMAA 1L0WA 3V4GA 3H3VL 2E2IC 3GTOK 5C4JK 4A3FK 1SFOA 1O29A 1TWHC 4A3DC 2NVXC 3GTOC 3I4NC 2NVTK 4Q5SA 3HOWK 1O2AA 1TWGK 2NVXK 2PMZL 4P9SA 1ISEA 4A3IK 1J6VA 3S1RC 1K83A 1I6HK 3LAJA 4A3CK 2WAQL 2E2JK 4WJ4A 4KASA 2WB1L 4KB2A 4A3EK 4XLPA 1Y1WC 2FQTA 1K83C 1WCMA 5IYCC 3A8JA 3S2HC 4WJ3M 1PJ7A 3GEEA 4QIWD 3GTMK 3CAGA 1JVIA 3SZYA 3S1MC 4PABA 4G0UA 3LAPA 5IYCK 3FHZA 3RZDK 1JQWA 4KMDA 2E2IA 4KATA 5TJ3A 4BLBA 1YX2A 2XCRB 1ZBSA 1F7VA 4KM8A 3TFHA 5EGHA 4G7ZA 3GTLA 3TFJA 4BY7K 3GTGK 1I3QA 1TWCC 3IPJA 2JA8C 2GAGC 4BY1C 3L4KA 1TWCA 2Y0SD 4ILDA 5C4XK 2CFAA 2VUMA 4G7HA 1TWGC 3GTLC 2EBBA 1SFOC 2E2JC 4KM9A 1EK8A 1WCMC 3H0GA 2PPBA 4OINA 4A3JC 3FOEA 5M5WK 4LJZA 1XXAA 4KMUA 2V6TA 4LR2A 4C3JK 3Q3QA 4KAWX 3GTLK 5L46A 2B63C 4XSZA 2FQOA 5CJ9A 4J3NA 1BGWA 5IYBC 3CQZA 4YFNA 5IOQA 1Y1VA 5C4JC 4A3FC 3WODA 3S14K 1XPPA 3FKIK 4X6AC 4C3JC 4XLNA 1TWFK 4A3KK 3S16K 1F7UA 4O2DA 1DD5A 1WIHA 2NVYA 4GFQA 1YNNA 2JA7A 2R93A 4BY7C 5JVOA 4A3BK 1IQ0A 4A3GC 3GTKA 3GTJC 3PO3K 1SFOK 3S0XA 2BE5A 2A6EA 2R93K 2JA6K 4A3BC 1WOPA 5M5YK 2NVXA 4P5AA 1K83K 5TMFA 4NOIA 3S1MK 3GTPC 4A3EC 2JA5C 3AD9C 3K7AC 5CHPA 1WORA 5FJ8K 1IS1A 3HOYK 2RH6A 3RZDC 3G4CA 2ZFZA 1SMYA 4OIOA 5EGEA 2GSUA 3EQLA 3HOZK 1PJ6A 5C3EC 1VH2A 4QJVB 2NVTC 4OIRA 4LK0A 4Y7NK 3FOFA 3GIRA 1V5VA 4GTEA 1ZQ1C 4FZBA 2NVQC 3RZOC 1TWAC 1WQGA 1Y1WK 4Y52K 1TWFC 4KDDA 4A3KC 4XCHA 1Y1VK 3I4NK 3S17K 4PAAA 2NVQK 2R7ZC 2D6FC 4C3HC 2PMZD 4JK1A 4MEXA 4Y7NC 2E2HC 4BXXC 4DDQA 4C3HK 1XXBA 2A69A 3G4AA 3HOVC 2P8TA 1R9TA 4OIPA 1EI6A 3AH5A
chains in the Genus database with same CATH topology
1J6VA 1INNA 1JQWA 1YCLA 1VH2A 1J6XA 1VGXA 2FQOA 1VJEA 2FQTA 1J6WA 1JOEA 4XCHA 1JVIA 5E68A 1J98A 1IE0A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1J6V A;  1INN A;  1JQW A;  1YCL A;  1VH2 A;  1J6X A;  1VGX A;  2FQO A;  1VJE A;  2FQT A;  1J6W A;  1JOE A;  4XCH A;  1JVI A;  5E68 A;  1J98 A;  1IE0 A; 
#chains in the Genus database with same CATH topology
 3S1Q K;  3TTG A;  4BBR K;  3HOZ C;  4LLG A;  4G0W A;  3OPF A;  4BLA A;  3GTJ A;  4AYB D;  2KWA A;  4AH6 A;  3AD7 C;  3HOX C;  5TMC A;  1I50 C;  1TWF A;  2YU9 A;  2WB1 D;  3M3Y C;  5M5X K;  3AQP A;  1ZVU A;  5IOR A;  4A3I C;  3GDZ A;  1RU0 A;  3S1R K;  1BDF A;  1J98 A;  1WSR A;  2JH3 A;  3GTQ C;  2Y0S L;  3BUE A;  3L4J A;  1B4A A;  4QIW L;  4C3I K;  2PA8 L;  4GZY A;  2CW0 A;  4A3L C;  3AQO A;  3S2H K;  4BXX K;  1X31 C;  3GTM A;  1IE0 A;  4KB4 A;  1YCL A;  2R92 C;  4A3M C;  1DCP A;  1XZP A;  4GT9 A;  1J6X A;  4FM9 A;  3S14 C;  3GTP A;  2GSN A;  3GTG A;  3S1Q C;  1J6W A;  1EQR A;  5M3F K;  3HOU C;  4A3L K;  5IYB K;  4Q4Z A;  3HKZ L;  2E2I K;  3HOW C;  1Y1V C;  3I4M C;  3CQZ C;  1TWA K;  4Y52 C;  1TWH K;  4A3D K;  3BP3 A;  3T01 A;  2P5M A;  4A3M K;  4BBS K;  1O27 A;  1B4B A;  4GTC A;  4C2M C;  1Y1W A;  2NVY C;  4YFX A;  1HI9 A;  3HOY C;  2WAQ D;  3S17 C;  3HOX K;  5IP9 K;  1WOO A;  1IL2 A;  5IYD K;  1O25 A;  4BY1 K;  2W7V A;  1AB4 A;  3MML B;  2B63 A;  5C3E K;  5HL8 A;  3GTO A;  1TWH A;  4KAR A;  1ZYR A;  2Y3P A;  4P5B A;  2RGR A;  1IBA A;  3OEP A;  1YNJ A;  3S16 C;  1TWG A;  3AD8 C;  4C45 A;  3S1N K;  3GEI A;  2A6H A;  1IW7 A;  2A68 A;  2ZUF A;  3N3Y A;  1USO A;  4XSX A;  4G7O A;  1I3Q C;  3M4O K;  4A93 C;  3I4M K;  2O5I A;  5IP9 C;  4GTB A;  4A3C C;  2JA6 A;  2PHC B;  1O2F B;  3GTJ K;  2NVY K;  4GTD A;  3T02 A;  4YFK A;  1I6V A;  4GTF A;  2YU9 C;  1O2B A;  4YG2 A;  4KN7 A;  1EH1 A;  3M4O C;  4ZH4 A;  3RZO K;  4LQY A;  1VRQ C;  2JA8 K;  3HKZ D;  2R7Z K;  3GTQ A;  1O24 A;  2JA5 K;  3S2D C;  3VA7 A;  2V6U A;  5C44 K;  1I50 A;  1ZXO A;  4A3J K;  1XXC A;  3ORE A;  4G0V A;  2R92 A;  3PO3 C;  4MEY A;  2CFA B;  3GTM C;  1G51 A;  3GTP K;  1I3Q K;  1WOS A;  3S15 C;  4GTL A;  1USM A;  3N0C A;  2ZUE A;  5FLM K;  3GTG C;  1WQH A;  3TFI A;  5E68 A;  1R9T K;  1TWA A;  4KMH A;  3NUH A;  5FLM C;  1I6H C;  2XCO A;  4BBS C;  1XZP B;  2E2H A;  4QJV A;  4KC6 A;  3CQZ K;  3HOV K;  4A3G K;  1WQF A;  4BBR C;  3H3V D;  1XZQ B;  5IOT A;  3DXJ A;  1INN A;  2JA7 K;  3LPX A;  1WCM K;  5D4D A;  3QX3 A;  3S2D K;  4GTA A;  3A8I A;  3FKI C;  4KN4 A;  1WSV A;  4M1X A;  4OIQ A;  4X6A K;  2YU9 K;  2O5J A;  2E2H K;  3GSI A;  1JOE A;  1F9N A;  1C0A A;  2XCQ A;  3GTK C;  3SZZ A;  2GSO A;  1VJE A;  5C4X C;  2JA7 C;  3HOU K;  2JA5 A;  5M3M K;  3FKI A;  1HQM A;  3N0B A;  3PO2 C;  4BKW A;  4C3I C;  1R9T C;  4A93 K;  1GE9 A;  3ERE D;  4WIL A;  3H0G K;  1UV7 A;  3T00 A;  1BS2 A;  2R92 K;  1KQ4 A;  5IOS A;  5IP7 K;  3GEH A;  1TWC K;  1EFW A;  3S1N C;  4AYB L;  1BJT A;  1XZQ A;  1PJ5 A;  3BP8 C;  2R7Z A;  2R93 C;  1I50 K;  2VUM K;  2GAH C;  5JFE A;  3K7A K;  1VGX A;  1DCO A;  3PO2 K;  5IP7 C;  3GTQ K;  4LK1 A;  4LOW A;  3S15 K;  2V6S A;  3H0G C;  4MQ9 A;  3M3Y K;  2JA6 C;  5IYD C;  3ADA C;  3HXA A;  2PA8 D;  3A8K A;  2VUM C;  1DCH A;  1O28 A;  4RMF A;  1VLO A;  3JST A;  1O26 A;  4C2M K;  1F93 A;  2B63 K;  5C44 C;  3GTK K;  4KMA A;  1L0W A;  3V4G A;  3H3V L;  2E2I C;  3GTO K;  5C4J K;  4A3F K;  1SFO A;  1O29 A;  1TWH C;  4A3D C;  2NVX C;  3GTO C;  3I4N C;  2NVT K;  4Q5S A;  3HOW K;  1O2A A;  1TWG K;  2NVX K;  2PMZ L;  4P9S A;  1ISE A;  4A3I K;  1J6V A;  3S1R C;  1K83 A;  1I6H K;  3LAJ A;  4A3C K;  2WAQ L;  2E2J K;  4WJ4 A;  4KAS A;  2WB1 L;  4KB2 A;  4A3E K;  4XLP A;  1Y1W C;  2FQT A;  1K83 C;  1WCM A;  5IYC C;  3A8J A;  3S2H C;  4WJ3 M;  1PJ7 A;  3GEE A;  4QIW D;  3GTM K;  3CAG A;  1JVI A;  3SZY A;  3S1M C;  4PAB A;  4G0U A;  3LAP A;  5IYC K;  3FHZ A;  3RZD K;  1JQW A;  4KMD A;  2E2I A;  4KAT A;  5TJ3 A;  4BLB A;  1YX2 A;  2XCR B;  1ZBS A;  1F7V A;  4KM8 A;  3TFH A;  5EGH A;  4G7Z A;  3GTL A;  3TFJ A;  4BY7 K;  3GTG K;  1I3Q A;  1TWC C;  3IPJ A;  2JA8 C;  2GAG C;  4BY1 C;  3L4K A;  1TWC A;  2Y0S D;  4ILD A;  5C4X K;  2CFA A;  2VUM A;  4G7H A;  1TWG C;  3GTL C;  2EBB A;  1SFO C;  2E2J C;  4KM9 A;  1EK8 A;  1WCM C;  3H0G A;  2PPB A;  4OIN A;  4A3J C;  3FOE A;  5M5W K;  4LJZ A;  1XXA A;  4KMU A;  2V6T A;  4LR2 A;  4C3J K;  3Q3Q A;  4KAW X;  3GTL K;  5L46 A;  2B63 C;  4XSZ A;  2FQO A;  5CJ9 A;  4J3N A;  1BGW A;  5IYB C;  3CQZ A;  4YFN A;  5IOQ A;  1Y1V A;  5C4J C;  4A3F C;  3WOD A;  3S14 K;  1XPP A;  3FKI K;  4X6A C;  4C3J C;  4XLN A;  1TWF K;  4A3K K;  3S16 K;  1F7U A;  4O2D A;  1DD5 A;  1WIH A;  2NVY A;  4GFQ A;  1YNN A;  2JA7 A;  2R93 A;  4BY7 C;  5JVO A;  4A3B K;  1IQ0 A;  4A3G C;  3GTK A;  3GTJ C;  3PO3 K;  1SFO K;  3S0X A;  2BE5 A;  2A6E A;  2R93 K;  2JA6 K;  4A3B C;  1WOP A;  5M5Y K;  2NVX A;  4P5A A;  1K83 K;  5TMF A;  4NOI A;  3S1M K;  3GTP C;  4A3E C;  2JA5 C;  3AD9 C;  3K7A C;  5CHP A;  1WOR A;  5FJ8 K;  1IS1 A;  3HOY K;  2RH6 A;  3RZD C;  3G4C A;  2ZFZ A;  1SMY A;  4OIO A;  5EGE A;  2GSU A;  3EQL A;  3HOZ K;  1PJ6 A;  5C3E C;  1VH2 A;  4QJV B;  2NVT C;  4OIR A;  4LK0 A;  4Y7N K;  3FOF A;  3GIR A;  1V5V A;  4GTE A;  1ZQ1 C;  4FZB A;  2NVQ C;  3RZO C;  1TWA C;  1WQG A;  1Y1W K;  4Y52 K;  1TWF C;  4KDD A;  4A3K C;  4XCH A;  1Y1V K;  3I4N K;  3S17 K;  4PAA A;  2NVQ K;  2R7Z C;  2D6F C;  4C3H C;  2PMZ D;  4JK1 A;  4MEX A;  4Y7N C;  2E2H C;  4BXX C;  4DDQ A;  4C3H K;  1XXB A;  2A69 A;  3G4A A;  3HOV C;  2P8T A;  1R9T A;  4OIP A;  1EI6 A;  3AH5 A; 
#chains in the Genus database with same CATH homology
 1J6V A;  1INN A;  1JQW A;  1YCL A;  1VH2 A;  1J6X A;  1VGX A;  2FQO A;  1VJE A;  2FQT A;  1J6W A;  1JOE A;  4XCH A;  1JVI A;  5E68 A;  1J98 A;  1IE0 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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#similar chains in the pdb database (?% sequence similarity)
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