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


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