2Y2XA

Crystal structure of pseudomonas aeruginosa opdk with vanillate
Total Genus 101
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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
101
sequence length
387
structure length
374
Chain Sequence
GFLEDAKTDLVLRNYYFNRDFLVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNSNSELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW
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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 Pseudomonas Aeruginosa Opdk with Vanillate
rcsb
source organism Pseudomonas aeruginosa pa01
molecule tags Membrane protein
molecule keywords VANILLATE PORIN OPDK
total genus 101
structure length 374
sequence length 387
chains with identical sequence B
ec nomenclature
pdb deposition date 2010-12-16

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03573 OprD outer membrane porin, OprD family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.160.10 Mainly Beta Beta Barrel Porin Porin 2y2xA01
5DL6A 3PORA 3A2SX 4AUIA 3VY9X 1HXUA 4FSPA 4FOZA 3JTYA 1PHOA 1GFOA 3VZTX 3T0SA 3UPGA 4LSIA 4GCQA 5JDPA 4GCPA 4LSHA 4JFBA 2XE2A 4LSFA 2J1NA 2OMFA 1OSMA 3SYSA 3WI4A 8PRNA 2Y0HA 3UU2A 1BH3A 2ODJA 2Y2XA 3POUA 1HXTA 1GFMA 4FRTA 3POQA 2XE5A 4FRXA 3VY8X 2QTKA 3VZUX 3SZVA 1MPFA 3WI5A 3EMNX 3T20A 2XE1A 3O0EA 1H6S1 1HXXA 3HW9A 2ZLDA 1GFQA 2FGQX 5DL7A 4C69X 1BT9A 5DL5A 2Y0LA 2O4VA 1E54A 2XG6A 2J4UP 4KR4A 3HWBA 4FMSA 4D5UA 3SY9A 1PRNA 6PRNA 1OPFA 2PORA 3SYBA 2PRNA 4KRAA 2FGRA 4LSEA 3T24A 5FVNA 1GFPA 5PRNA 1GFNA 3FYXA 3NSGA 3VZWX 3K19A 4D65A 2Y0KA 4GCSA 5DL8A 2K4TA 7PRNA 4FSOA 4D64A 3SY7A 2ZFGA 2XE3A 3POXA 4RJXA 3SZDA 3PRNA 4KR8A 4FT6A 4BUMX 4RJWA
chains in the Genus database with same CATH superfamily
2N2LA 5DL6A 3PORA 3A2SX 4FZNA 4N74A 4AUIA 5IYUA 3VY9X 1HXUA 4FSPA 3HOLA 4FOZA 2MHLA 4GHBA 1G90A 3JTYA 2MNHA 3PGRA 3VE1A 1PHOA 3LK2B 4GF4A 4O3YA 1GFOA 2F1VA 3VZTX 2M06A 1P4TA 2YNKA 5ADXK 3JCUO 3T0SA 3UPGA 3DWNA 4LSIA 4AYEC 4GCQA 1ZHTA 4XNKA 5T5FA 4GCPA 5JDPA 5B5EO 2K0LA 3AA0A 4LSHA 2R4NA 4JFBA 4U9CA 4B61A 2XE2A 3BRYA 1IZNA 4LSFA 5GTHO 2N2MA 3AA7B 2J1NA 2OMFA 3LK41 1Q9GA 4AKRA 1OSMA 3BS0A 3SYSA 4N58A 3WI4A 2W80C 1S5LO 5B66O 1ZHWA 1ORMA 5TISO 3AAEA 3A0BO 8PRNA 2Y0HA 3TZGA 1QJ9A 5KAFO 2WJRA 3UU2A 3VE2A 4RL9A 4FZLA 1BH3A 2ODJA 1Q9FA 5E79O 5GV0A 2KXPA 2Y2XA 3POUA 3QRCA 1HXTA 1GFMA 2F1CX 4FRTA 3POQA 2XE5A 3AA6B 3PQUA 4O3ZA 2W81C 4FUVA 2JQYA 4FRXA 5G26A 5GTIO 2IWVA 3LK3A 1ZHXA 2GE4A 3BRZA 1T16A 2QTKA 3AA0B 4PJ0O 3VY8X 1YS5A 3VZUX 4AYNA 5AFUK 3SZVA 4O4UA 4AZLA 1MPFA 1ZHZA 3HOEA 5AFUL 2KZ7A 3WI5A 4O49A 3G7GA 4PR7A 2XTRA 4AYDC 3EMNX 3T20A 2XE1A 2R89A 4AFKA 3O0EA 3DZMA 4O3WA 5G38A 1H6S1 1HXXA 1MM4A 4AYMC 4AYID 2M07A 2WJQA 3HW9A 2ERVA 2LHFA 2JMMA 2ZLDA 3NJTA 4G76A 4QQ1A 3PGUA 4XNLA 5D5DA 2X9KA 4N75A 4PUXA 3KVDD 3AAEB 3V8UA 1GFQA 2FGQX 5DL7A 4C69X 1BT9A 3DWOX 2WVPA 2Y0LA 5DL5A 2R4LA 3A0HO 2O4VA 1E54A 4K3BA 4C00A 1T1LA 2XG6A 4AKMA 4RLBA 4KR4A 2J4UP 2KXPB 3HWBA 4E1SA 3GP6A 3AA1B 4FMSA 4D5UA 4Z3TA 4FQEA 1QJ8A 3SY9A 4F4BA 2KZ7B 1PRNA 2R88A 2XTQA 3AA6A 4FZMA 6PRNA 1OPFA 2PORA 3SYBA 4N59A 2PRNA 3AAAB 3LK3B 4KRAA 4UB8O 3UAQA 2F1TA 4K3CA 4CTDA 2FGRA 2YPVA 4LSEA 3WU2O 1THQA 4G75A 2AXTO 3T24A 5FVNA 4C4VB 1GFPA 2R4PA 2IWWA 5PRNA 1GFNA 3FYXA 4C4VA 3NSGA 4JCHA 3VZWX 4FESA 3K19A 5EE2A 2R8AA 4D65A 5KAIO 2Y0KA 4GCSA 5G39A 5DL8A 2K4TA 4D64A 4UB6O 7PRNA 2XMXA 3DA3A 3PGSA 4O3XB 3LK2A 4FSOA 4IL6O 3RBHA 3SY7A 1IZNB 2Y7SA 3AA1A 3AA7A 4RLCA 2ZFGA 3KZIO 1QJPA 3QRAA 3PQSA 5ADXL 2XE3A 3POXA 4RJXA 3LK42 3AAAA 2LFUA 3SZDA 3PRNA 2KDYA 2KC0A 3C5OA 1ZHYA 4O4XA 4E1TA 1MM5A 5H2FO 2R4OA 5G3AA 1BXWA 4KR8A 4FT6A 2X27X 4BUMX 3DA4A 4AKRB 3PF1A 4RJWA
chains in the Genus database with same CATH topology
2N2LA 5DL6A 3PORA 3A2SX 4FZNA 4AUIA 5IYUA 3VY9X 1HXUA 4FSPA 3HOLA 4FOZA 2MHLA 4GHBA 1G90A 3JTYA 2MNHA 3VE1A 1PHOA 3LK2B 4GF4A 4O3YA 1GFOA 2F1VA 3VZTX 2M06A 1P4TA 2YNKA 5ADXK 3T0SA 3UPGA 4LSIA 4AYEC 4GCQA 1ZHTA 4XNKA 5T5FA 4GCPA 5JDPA 2K0LA 3AA0A 4LSHA 4U9CA 4JFBA 4B61A 2XE2A 1IZNA 4LSFA 2N2MA 3AA7B 2J1NA 2OMFA 3LK41 1Q9GA 4AKRA 1OSMA 3SYSA 3WI4A 4N58A 2W80C 1ZHWA 1ORMA 3AAEA 8PRNA 2Y0HA 3TZGA 1QJ9A 3UU2A 3VE2A 4RL9A 4FZLA 1BH3A 2ODJA 1Q9FA 5GV0A 2KXPA 2Y2XA 3POUA 3QRCA 1HXTA 1GFMA 4FRTA 3POQA 2XE5A 3AA6B 3PQUA 4O3ZA 2W81C 4FUVA 5G26A 4FRXA 3LK3A 1ZHXA 2GE4A 3VY8X 3AA0B 2QTKA 4AYNA 1YS5A 3VZUX 3SZVA 4O4UA 4AZLA 1MPFA 1ZHZA 3HOEA 5AFUL 2KZ7A 3WI5A 4O49A 3G7GA 2XTRA 4AYDC 3EMNX 3T20A 2XE1A 4AFKA 3O0EA 4O3WA 1H6S1 1HXXA 1MM4A 4AYMC 4AYID 2M07A 3HW9A 2ERVA 2LHFA 2JMMA 2ZLDA 4G76A 4QQ1A 4XNLA 5D5DA 4PUXA 3KVDD 3AAEB 3V8UA 1GFQA 2FGQX 5DL7A 4C69X 1BT9A 5DL5A 2Y0LA 2O4VA 1E54A 2XG6A 4AKMA 4RLBA 4KR4A 2J4UP 2KXPB 3HWBA 4E1SA 3GP6A 3AA1B 4FMSA 4D5UA 4Z3TA 3SY9A 1QJ8A 4F4BA 5AFUK 2XTQA 2KZ7B 1PRNA 3AA6A 4FZMA 6PRNA 1OPFA 2PORA 3SYBA 4N59A 2PRNA 3AAAB 3LK3B 4KRAA 3UAQA 2F1TA 2FGRA 2YPVA 4LSEA 1THQA 4G75A 3T24A 5FVNA 1GFPA 5PRNA 1GFNA 3FYXA 3NSGA 4JCHA 3VZWX 4FESA 3K19A 5EE2A 4D65A 2Y0KA 4GCSA 5DL8A 2K4TA 7PRNA 2XMXA 3DA3A 4O3XB 3LK2A 4FSOA 3RBHA 3SY7A 4D64A 1IZNB 2Y7SA 3AA1A 3AA7A 4RLCA 2ZFGA 1QJPA 3QRAA 3PQSA 5ADXL 2XE3A 3POXA 4RJXA 3LK42 3AAAA 2LFUA 3SZDA 3PRNA 2KDYA 2KC0A 3C5OA 1ZHYA 4O4XA 4E1TA 1MM5A 1BXWA 4KR8A 4FT6A 2X27X 4BUMX 3DA4A 4AKRB 4RJWA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5DL6 A;  3POR A;  3A2S X;  4AUI A;  3VY9 X;  1HXU A;  4FSP A;  4FOZ A;  3JTY A;  1PHO A;  1GFO A;  3VZT X;  3T0S A;  3UPG A;  4LSI A;  4GCQ A;  5JDP A;  4GCP A;  4LSH A;  4JFB A;  2XE2 A;  4LSF A;  2J1N A;  2OMF A;  1OSM A;  3SYS A;  3WI4 A;  8PRN A;  2Y0H A;  3UU2 A;  1BH3 A;  2ODJ A;  2Y2X A;  3POU A;  1HXT A;  1GFM A;  4FRT A;  3POQ A;  2XE5 A;  4FRX A;  3VY8 X;  2QTK A;  3VZU X;  3SZV A;  1MPF A;  3WI5 A;  3EMN X;  3T20 A;  2XE1 A;  3O0E A;  1H6S 1;  1HXX A;  3HW9 A;  2ZLD A;  1GFQ A;  2FGQ X;  5DL7 A;  4C69 X;  1BT9 A;  5DL5 A;  2Y0L A;  2O4V A;  1E54 A;  2XG6 A;  2J4U P;  4KR4 A;  3HWB A;  4FMS A;  4D5U A;  3SY9 A;  1PRN A;  6PRN A;  1OPF A;  2POR A;  3SYB A;  2PRN A;  4KRA A;  2FGR A;  4LSE A;  3T24 A;  5FVN A;  1GFP A;  5PRN A;  1GFN A;  3FYX A;  3NSG A;  3VZW X;  3K19 A;  4D65 A;  2Y0K A;  4GCS A;  5DL8 A;  2K4T A;  7PRN A;  4FSO A;  4D64 A;  3SY7 A;  2ZFG A;  2XE3 A;  3POX A;  4RJX A;  3SZD A;  3PRN A;  4KR8 A;  4FT6 A;  4BUM X;  4RJW A; 
#chains in the Genus database with same CATH topology
 2N2L A;  5DL6 A;  3POR A;  3A2S X;  4FZN A;  4N74 A;  4AUI A;  5IYU A;  3VY9 X;  1HXU A;  4FSP A;  3HOL A;  4FOZ A;  2MHL A;  4GHB A;  1G90 A;  3JTY A;  2MNH A;  3PGR A;  3VE1 A;  1PHO A;  3LK2 B;  4GF4 A;  4O3Y A;  1GFO A;  2F1V A;  3VZT X;  2M06 A;  1P4T A;  2YNK A;  5ADX K;  3JCU O;  3T0S A;  3UPG A;  3DWN A;  4LSI A;  4AYE C;  4GCQ A;  1ZHT A;  4XNK A;  5T5F A;  4GCP A;  5JDP A;  5B5E O;  2K0L A;  3AA0 A;  4LSH A;  2R4N A;  4JFB A;  4U9C A;  4B61 A;  2XE2 A;  3BRY A;  1IZN A;  4LSF A;  5GTH O;  2N2M A;  3AA7 B;  2J1N A;  2OMF A;  3LK4 1;  1Q9G A;  4AKR A;  1OSM A;  3BS0 A;  3SYS A;  4N58 A;  3WI4 A;  2W80 C;  1S5L O;  5B66 O;  1ZHW A;  1ORM A;  5TIS O;  3AAE A;  3A0B O;  8PRN A;  2Y0H A;  3TZG A;  1QJ9 A;  5KAF O;  2WJR A;  3UU2 A;  3VE2 A;  4RL9 A;  4FZL A;  1BH3 A;  2ODJ A;  1Q9F A;  5E79 O;  5GV0 A;  2KXP A;  2Y2X A;  3POU A;  3QRC A;  1HXT A;  1GFM A;  2F1C X;  4FRT A;  3POQ A;  2XE5 A;  3AA6 B;  3PQU A;  4O3Z A;  2W81 C;  4FUV A;  2JQY A;  4FRX A;  5G26 A;  5GTI O;  2IWV A;  3LK3 A;  1ZHX A;  2GE4 A;  3BRZ A;  1T16 A;  2QTK A;  3AA0 B;  4PJ0 O;  3VY8 X;  1YS5 A;  3VZU X;  4AYN A;  5AFU K;  3SZV A;  4O4U A;  4AZL A;  1MPF A;  1ZHZ A;  3HOE A;  5AFU L;  2KZ7 A;  3WI5 A;  4O49 A;  3G7G A;  4PR7 A;  2XTR A;  4AYD C;  3EMN X;  3T20 A;  2XE1 A;  2R89 A;  4AFK A;  3O0E A;  3DZM A;  4O3W A;  5G38 A;  1H6S 1;  1HXX A;  1MM4 A;  4AYM C;  4AYI D;  2M07 A;  2WJQ A;  3HW9 A;  2ERV A;  2LHF A;  2JMM A;  2ZLD A;  3NJT A;  4G76 A;  4QQ1 A;  3PGU A;  4XNL A;  5D5D A;  2X9K A;  4N75 A;  4PUX A;  3KVD D;  3AAE B;  3V8U A;  1GFQ A;  2FGQ X;  5DL7 A;  4C69 X;  1BT9 A;  3DWO X;  2WVP A;  2Y0L A;  5DL5 A;  2R4L A;  3A0H O;  2O4V A;  1E54 A;  4K3B A;  4C00 A;  1T1L A;  2XG6 A;  4AKM A;  4RLB A;  4KR4 A;  2J4U P;  2KXP B;  3HWB A;  4E1S A;  3GP6 A;  3AA1 B;  4FMS A;  4D5U A;  4Z3T A;  4FQE A;  1QJ8 A;  3SY9 A;  4F4B A;  2KZ7 B;  1PRN A;  2R88 A;  2XTQ A;  3AA6 A;  4FZM A;  6PRN A;  1OPF A;  2POR A;  3SYB A;  4N59 A;  2PRN A;  3AAA B;  3LK3 B;  4KRA A;  4UB8 O;  3UAQ A;  2F1T A;  4K3C A;  4CTD A;  2FGR A;  2YPV A;  4LSE A;  3WU2 O;  1THQ A;  4G75 A;  2AXT O;  3T24 A;  5FVN A;  4C4V B;  1GFP A;  2R4P A;  2IWW A;  5PRN A;  1GFN A;  3FYX A;  4C4V A;  3NSG A;  4JCH A;  3VZW X;  4FES A;  3K19 A;  5EE2 A;  2R8A A;  4D65 A;  5KAI O;  2Y0K A;  4GCS A;  5G39 A;  5DL8 A;  2K4T A;  4D64 A;  4UB6 O;  7PRN A;  2XMX A;  3DA3 A;  3PGS A;  4O3X B;  3LK2 A;  4FSO A;  4IL6 O;  3RBH A;  3SY7 A;  1IZN B;  2Y7S A;  3AA1 A;  3AA7 A;  4RLC A;  2ZFG A;  3KZI O;  1QJP A;  3QRA A;  3PQS A;  5ADX L;  2XE3 A;  3POX A;  4RJX A;  3LK4 2;  3AAA A;  2LFU A;  3SZD A;  3PRN A;  2KDY A;  2KC0 A;  3C5O A;  1ZHY A;  4O4X A;  4E1T A;  1MM5 A;  5H2F O;  2R4O A;  5G3A A;  1BXW A;  4KR8 A;  4FT6 A;  2X27 X;  4BUM X;  3DA4 A;  4AKR B;  3PF1 A;  4RJW A; 
#chains in the Genus database with same CATH homology
 2N2L A;  5DL6 A;  3POR A;  3A2S X;  4FZN A;  4AUI A;  5IYU A;  3VY9 X;  1HXU A;  4FSP A;  3HOL A;  4FOZ A;  2MHL A;  4GHB A;  1G90 A;  3JTY A;  2MNH A;  3VE1 A;  1PHO A;  3LK2 B;  4GF4 A;  4O3Y A;  1GFO A;  2F1V A;  3VZT X;  2M06 A;  1P4T A;  2YNK A;  5ADX K;  3T0S A;  3UPG A;  4LSI A;  4AYE C;  4GCQ A;  1ZHT A;  4XNK A;  5T5F A;  4GCP A;  5JDP A;  2K0L A;  3AA0 A;  4LSH A;  4U9C A;  4JFB A;  4B61 A;  2XE2 A;  1IZN A;  4LSF A;  2N2M A;  3AA7 B;  2J1N A;  2OMF A;  3LK4 1;  1Q9G A;  4AKR A;  1OSM A;  3SYS A;  3WI4 A;  4N58 A;  2W80 C;  1ZHW A;  1ORM A;  3AAE A;  8PRN A;  2Y0H A;  3TZG A;  1QJ9 A;  3UU2 A;  3VE2 A;  4RL9 A;  4FZL A;  1BH3 A;  2ODJ A;  1Q9F A;  5GV0 A;  2KXP A;  2Y2X A;  3POU A;  3QRC A;  1HXT A;  1GFM A;  4FRT A;  3POQ A;  2XE5 A;  3AA6 B;  3PQU A;  4O3Z A;  2W81 C;  4FUV A;  5G26 A;  4FRX A;  3LK3 A;  1ZHX A;  2GE4 A;  3VY8 X;  3AA0 B;  2QTK A;  4AYN A;  1YS5 A;  3VZU X;  3SZV A;  4O4U A;  4AZL A;  1MPF A;  1ZHZ A;  3HOE A;  5AFU L;  2KZ7 A;  3WI5 A;  4O49 A;  3G7G A;  2XTR A;  4AYD C;  3EMN X;  3T20 A;  2XE1 A;  4AFK A;  3O0E A;  4O3W A;  1H6S 1;  1HXX A;  1MM4 A;  4AYM C;  4AYI D;  2M07 A;  3HW9 A;  2ERV A;  2LHF A;  2JMM A;  2ZLD A;  4G76 A;  4QQ1 A;  4XNL A;  5D5D A;  4PUX A;  3KVD D;  3AAE B;  3V8U A;  1GFQ A;  2FGQ X;  5DL7 A;  4C69 X;  1BT9 A;  5DL5 A;  2Y0L A;  2O4V A;  1E54 A;  2XG6 A;  4AKM A;  4RLB A;  4KR4 A;  2J4U P;  2KXP B;  3HWB A;  4E1S A;  3GP6 A;  3AA1 B;  4FMS A;  4D5U A;  4Z3T A;  3SY9 A;  1QJ8 A;  4F4B A;  5AFU K;  2XTQ A;  2KZ7 B;  1PRN A;  3AA6 A;  4FZM A;  6PRN A;  1OPF A;  2POR A;  3SYB A;  4N59 A;  2PRN A;  3AAA B;  3LK3 B;  4KRA A;  3UAQ A;  2F1T A;  2FGR A;  2YPV A;  4LSE A;  1THQ A;  4G75 A;  3T24 A;  5FVN A;  1GFP A;  5PRN A;  1GFN A;  3FYX A;  3NSG A;  4JCH A;  3VZW X;  4FES A;  3K19 A;  5EE2 A;  4D65 A;  2Y0K A;  4GCS A;  5DL8 A;  2K4T A;  7PRN A;  2XMX A;  3DA3 A;  4O3X B;  3LK2 A;  4FSO A;  3RBH A;  3SY7 A;  4D64 A;  1IZN B;  2Y7S A;  3AA1 A;  3AA7 A;  4RLC A;  2ZFG A;  1QJP A;  3QRA A;  3PQS A;  5ADX L;  2XE3 A;  3POX A;  4RJX A;  3LK4 2;  3AAA A;  2LFU A;  3SZD A;  3PRN A;  2KDY A;  2KC0 A;  3C5O A;  1ZHY A;  4O4X A;  4E1T A;  1MM5 A;  1BXW A;  4KR8 A;  4FT6 A;  2X27 X;  4BUM X;  3DA4 A;  4AKR B;  4RJW 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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