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


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