3SYBA

Crystal structure of pseudomonas aeruginosa occd3 (opdp)
Total Genus 118
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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
118
sequence length
452
structure length
408
Chain Sequence
PAPDNPSYAAEVQSIPSVAKPIKGQAGATGLVEGQSLTLTTRNFYSRENQRNAWVQGTVLKYSSGYTQGTVGFGFDVAAFNEIALGEWSKLGVANIRLRASNTEFKAGRFLVNTPVFSYIDNRALPSSFTGFAVTSEELDNLSLQAGSFRKVSPRTGSGDEDMTTEYGTRQVKGDRLNYLGGNYKPLDGLEISLYGSHFQDVWNQYYLGVTHDIGLENGIALRTAFNGYHTGDTGAREAGYIDNDTWSLAFTLGHRAHALTLAYQQVDGNEYFDYVHETSAIFLANSMLADYNSPNEKSAQIRYETDWSYYGVPGLSTGVWYVKGWDIDGTHYDGDRNGAYGNYAEVRAQDGEKHHELGLMAAYKVQNGPIKDSTFKLTYMMHKASQNQIDGSVNELRLVSTFPFNLL
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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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molecule tags Membrane protein
molecule keywords Glycine-glutamate dipeptide porin OpdP
publication title Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
pubmed doi rcsb
source organism Pseudomonas aeruginosa
total genus 118
structure length 408
sequence length 452
ec nomenclature
pdb deposition date 2011-07-16

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 3sybA00
3T0SA 1GFQA 4KR8A 4FRXA 3T20A 4BUMX 1OSMA 3VY8X 1PRNA 2XE3A 4FSOA 1H6S1 2O4VA 2XE2A 4KRAA 2Y0KA 3SZVA 4LSIA 2FGQX 3A2SX 3SYSA 2XE5A 8PRNA 3HW9A 3SY9A 3EMNX 4LSHA 3POXA 4FSPA 4C69X 4RJWA 4RJXA 1GFPA 3UPGA 2XG6A 1HXUA 4GCPA 5PRNA 4LSFA 3VZUX 4LSEA 1HXXA 3WI4A 4GCSA 1GFOA 3PORA 4D5UA 5DL8A 2Y0LA 3VY9X 2QTKA 2Y2XA 5JDPA 3HWBA 7PRNA 1MPFA 1HXTA 2K4TA 4KR4A 3NSGA 3SYBA 1GFNA 4D65A 3POUA 4GCQA 5DL7A 3O0EA 3SZDA 2J1NA 2XE1A 3SY7A 3T24A 3UU2A 3VZWX 5DL6A 6PRNA 1E54A 3JTYA 2OMFA 2ZLDA 1BT9A 2FGRA 2ODJA 2ZFGA 2PRNA 1GFMA 4FOZA 4FT6A 3VZTX 4D64A 5DL5A 3WI5A 1PHOA 2Y0HA 5FVNA 4FMSA 1BH3A 4JFBA 3K19A 2PORA 4AUIA 2J4UP 3PRNA 1OPFA 3FYXA 3POQA 4FRTA
chains in the Genus database with same CATH superfamily
1BXWA 3VE1A 3T0SA 1GFQA 4KR8A 4K3CA 2F1CX 3LK3A 4FRXA 3T20A 5B66O 4BUMX 2AXTO 1OSMA 3VY8X 4U9CA 5GTHO 2M07A 2R4PA 2KDYA 2X9KA 1T1LA 1PRNA 2XE3A 4FSOA 1H6S1 2O4VA 2XE2A 2MHLA 4KRAA 2Y0KA 5IYUA 3SZVA 3DWNA 2FGQX 3A2SX 4LSIA 2XE5A 4FZLA 3SYSA 4CTDA 5AFUL 3HW9A 3QRCA 8PRNA 3AAEA 3SY9A 2JMMA 1YS5A 2W81C 3HOEA 4Z3TA 3QRAA 3GP6A 1ZHXA 2KXPA 4N59A 1MM4A 3BS0A 1ZHTA 3RBHA 3DZMA 3EMNX 1QJ9A 4FZNA 4N75A 4QQ1A 4K3BA 2KZ7B 1Q9GA 3A0BO 4FQEA 4N58A 4LSHA 3POXA 4FSPA 4GHBA 2GE4A 2R8AA 2N2MA 3BRYA 4AFKA 4C69X 1MM5A 4F4BA 4RJWA 1Q9FA 4RJXA 5G3AA 1GFPA 1ZHYA 4AKMA 3UPGA 2R89A 2XG6A 4O4XA 4E1TA 5T5FA 5ADXL 2IWWA 4RLCA 1HXUA 4GCPA 3TZGA 5PRNA 3WU2O 2LFUA 3AAAA 5E79O 4AYDC 4O3YA 2N2LA 2K0LA 5TISO 4LSFA 3VZUX 1IZNB 3DA4A 3WI5A 2XMXA 4G75A 5GTIO 2WJRA 1ORMA 4FZMA 4LSEA 5GV0A 3PQSA 4O49A 4G76A 3VE2A 1HXXA 4PR7A 3WI4A 4RLBA 1QJPA 2KZ7A 3AA7B 5EE2A 3AA6B 4GCSA 3LK2B 5ADXK 5D5DA 4RL9A 4AYNA 3A0HO 1GFOA 4AKRB 2IWVA 5AFUK 4FRTA 4C4VB 3PQUA 2MNHA 4D64A 4PJ0O 1G90A 1ZHZA 3HOLA 3PORA 4AZLA 1T16A 4D5UA 5DL8A 2Y0LA 3VY9X 3LK41 2QTKA 1S5LO 2Y2XA 3DWOX 5KAFO 5JDPA 4O3ZA 3HWBA 1QJ8A 2LHFA 3AA0B 3UAQA 7PRNA 4XNKA 2XTQA 1MPFA 1HXTA 2K4TA 3FYXA 3KZIO 4KR4A 3BRZA 3NSGA 5G39A 5B5EO 2R88A 2YPVA 3C5OA 3SYBA 1GFNA 4AYID 4D65A 2JQYA 3POUA 4GCQA 5DL7A 3O0EA 4AYMC 3AA7A 3AA1B 3SZDA 3AA6A 5KAIO 3LK2A 4FESA 2J1NA 2M06A 1P4TA 2XE1A 3SY7A 3T24A 3UU2A 3VZWX 2Y7SA 2WVPA 4XNLA 4PUXA 5DL6A 4JCHA 4AKRA 3PF1A 1E54A 4IL6O 3JTYA 5G26A 4C4VA 6PRNA 2ERVA 5H2FO 3PGSA 2ZLDA 4O3XB 2KC0A 4B61A 3LK42 4O4UA 3LK3B 1ZHWA 4FUVA 1BT9A 2FGRA 2ODJA 4GF4A 3AA0A 5G38A 4AYEC 2ZFGA 2PRNA 1GFMA 4FOZA 4C00A 4FT6A 3VZTX 4E1SA 2X27X 2XTRA 2WJQA 2R4NA 3AAAB 1IZNA 4O3WA 2F1VA 1THQA 2YNKA 5DL5A 1PHOA 2Y0HA 5FVNA 3G7GA 2F1TA 3JCUO 1BH3A 3AA1A 3NJTA 3AAEB 3PGUA 3K19A 4FMSA 3KVDD 4JFBA 2PORA 2W80C 4N74A 4UB6O 4AUIA 3PGRA 4UB8O 3V8UA 3DA3A 3PRNA 2J4UP 2KXPB 1OPFA 2R4LA 2OMFA 3POQA 2R4OA
chains in the Genus database with same CATH topology
1BXWA 3VE1A 3T0SA 1GFQA 4KR8A 3LK3A 4FRXA 3T20A 4BUMX 1OSMA 3VY8X 4U9CA 2M07A 2KDYA 1PRNA 2XE3A 4FSOA 1H6S1 2O4VA 2XE2A 2MHLA 4KRAA 2Y0KA 5IYUA 3SZVA 4LSIA 2FGQX 3A2SX 3SYSA 2XE5A 4FZLA 5AFUL 8PRNA 3HW9A 3QRCA 3AAEA 3SY9A 2JMMA 1YS5A 2W81C 3HOEA 4Z3TA 3QRAA 3GP6A 1ZHXA 2KXPA 4N59A 1MM4A 1ZHTA 3RBHA 3EMNX 1QJ9A 4FZNA 4QQ1A 2KZ7B 1Q9GA 4N58A 4LSHA 3POXA 4FSPA 4GHBA 2GE4A 2N2MA 4AFKA 4C69X 1MM5A 4F4BA 4RJWA 1Q9FA 4RJXA 1GFPA 1ZHYA 4AKMA 3UPGA 2XG6A 4O4XA 4E1TA 5T5FA 5ADXL 4RLCA 1HXUA 4GCPA 3TZGA 5PRNA 4AYDC 2LFUA 3AAAA 4O3YA 2N2LA 2K0LA 4LSFA 3VZUX 1IZNB 3DA4A 3WI5A 2XMXA 4G75A 1ORMA 4FZMA 4LSEA 5GV0A 3PQSA 4O49A 4G76A 3VE2A 1HXXA 3WI4A 4RLBA 1QJPA 2KZ7A 3AA7B 5EE2A 3AA6B 4GCSA 3LK2B 5ADXK 5D5DA 4RL9A 4AYNA 1GFOA 4AKRB 5AFUK 3PQUA 2MNHA 4D64A 1G90A 1ZHZA 3HOLA 3PORA 4AZLA 4D5UA 5DL8A 2Y0LA 3VY9X 3LK41 2QTKA 2Y2XA 5JDPA 4O3ZA 3HWBA 1QJ8A 2LHFA 3AA0B 3UAQA 7PRNA 4XNKA 2XTQA 1MPFA 1HXTA 2K4TA 3FYXA 4KR4A 3NSGA 2YPVA 3C5OA 3SYBA 1GFNA 4AYID 4D65A 3POUA 4GCQA 5DL7A 3O0EA 4AYMC 3AA7A 3AA1B 3SZDA 3AA6A 3LK2A 4FESA 2J1NA 2M06A 1P4TA 2XE1A 3SY7A 3T24A 3UU2A 3VZWX 2Y7SA 4XNLA 4AKRA 4PUXA 5DL6A 4JCHA 6PRNA 1E54A 5G26A 3JTYA 2ERVA 2ZLDA 4O3XB 2KC0A 4B61A 3LK42 4O4UA 3LK3B 1ZHWA 4FUVA 1BT9A 2FGRA 2ODJA 4GF4A 3AA0A 4AYEC 2ZFGA 2PRNA 1GFMA 4FOZA 4FT6A 3VZTX 4E1SA 2X27X 2XTRA 3AAAB 1IZNA 4O3WA 2F1VA 1THQA 2YNKA 5DL5A 1PHOA 2Y0HA 5FVNA 3G7GA 2F1TA 4FMSA 1BH3A 3AA1A 4JFBA 3AAEB 3K19A 3KVDD 2PORA 2W80C 4AUIA 3V8UA 3DA3A 3PRNA 2J4UP 2KXPB 1OPFA 2OMFA 3POQA 4FRTA
chains in the Genus database with same CATH homology


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