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
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.

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


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