3JTYA

Crystal structure of a benf-like porin from pseudomonas fluorescens pf-5
Total Genus 97
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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
97
sequence length
388
structure length
388
Chain Sequence
GFLEDAQANLTLRNFYFNRNFTNPTKAQGKAEEWTQSFILDAKSGFTQGTVGFGMDVLGLYSLKLDGGKGTGGTQLLPLDHDGRPADNFGRLGVAFKARLSQTEVKVGEWMPVLPILRSDDGRSLPQTFRGGQITSKEIAGLTLYGGQFRANSPRDDSSMSDMSMFGKAAFTSDRFNFQGAEYAFNDKRTQIALWNAQLKDIYSQQFINLIHSQPLGDWTLGANLGFFYGKEDGSARAGDMENRTWSGLFSAKYGGNTFYVGLQKLTGDSAWMRVNGTSGGTLANDSYNASYDNAKEKSWQVRHDYNFAALGVPGLTLMNRYISGSNVHTATVSDGKEWGRESEVAYTVQSGTLKNLNLKWRNSTMRRDFSNNEFDENRLIISYPLSL
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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 Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
pubmed doi rcsb
source organism Pseudomonas fluorescens pf-5
molecule tags Transport protein
molecule keywords BenF-like porin
total genus 97
structure length 388
sequence length 388
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2009-09-14

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 3jtyA01
3T24A 2Y2XA 3WI5A 5DL7A 3HW9A 4KR8A 1BT9A 1E54A 4LSFA 3POQA 2ODJA 1GFQA 4GCQA 3PORA 3SY9A 4LSEA 4LSHA 2FGQX 4FRXA 1HXUA 4FSOA 2ZLDA 2PORA 1GFMA 1MPFA 2XE3A 4FSPA 3SZVA 1PHOA 3JTYA 1GFOA 4BUMX 5DL5A 4FRTA 3SZDA 4KR4A 4FT6A 3SY7A 3T20A 3SYSA 1BH3A 2FGRA 5DL8A 3UU2A 2J4UP 4FMSA 7PRNA 2XE1A 2PRNA 3POXA 1OPFA 4GCSA 3A2SX 4C69X 1HXTA 3VZUX 5JDPA 3NSGA 3WI4A 4RJXA 5DL6A 5FVNA 1PRNA 1H6S1 2J1NA 3VZWX 3FYXA 6PRNA 4LSIA 3VY8X 2XG6A 2O4VA 3VZTX 4D64A 2XE2A 2QTKA 2OMFA 4GCPA 8PRNA 3K19A 2Y0HA 4D65A 4JFBA 2ZFGA 2Y0KA 3EMNX 2K4TA 3PRNA 2XE5A 4FOZA 3T0SA 3HWBA 1GFNA 2Y0LA 3SYBA 4KRAA 3VY9X 4AUIA 1OSMA 1GFPA 3UPGA 5PRNA 4RJWA 1HXXA 3O0EA 3POUA 4D5UA
chains in the Genus database with same CATH superfamily
3PGUA 3DWOX 3HOEA 5T5FA 1ZHTA 4GHBA 4N58A 4O3WA 3T24A 3TZGA 5AFUL 5G3AA 1IZNB 2Y2XA 3WI5A 4C4VA 1YS5A 3QRCA 4UB6O 3JCUO 5DL7A 5KAIO 3UAQA 3HW9A 4KR8A 1ZHWA 3LK2A 4D5UA 4Z3TA 5GTHO 1ZHYA 2X27X 1BT9A 1T1LA 4CTDA 5E79O 1E54A 4LSFA 3POQA 2ODJA 3AAEB 3DA4A 1GFQA 1MM4A 2M06A 4GCQA 2LHFA 3BRYA 3PORA 3SY9A 2XMXA 4LSEA 3LK3A 3AA1A 2YNKA 2R89A 2FGQX 4FRXA 1HXUA 2K0LA 4LSHA 4FSOA 2ZLDA 3RBHA 3AAEA 5GTIO 1Q9FA 4UB8O 2N2LA 2F1CX 1GFMA 2PORA 4C00A 1IZNA 4RLCA 4O4XA 5ADXK 3LK2B 1MPFA 1ZHXA 2XE3A 3PQUA 4FSPA 4PR7A 2WJQA 3SZVA 3PQSA 1P4TA 1PHOA 2X9KA 4AZLA 3A0HO 2KDYA 3JTYA 1GFOA 4BUMX 5DL5A 4FRTA 3SZDA 4KR4A 5G39A 4N74A 2R88A 3AA6A 3LK3B 4FT6A 5TISO 1Q9GA 4AYDC 3G7GA 4IL6O 4PJ0O 4E1TA 3BRZA 3PF1A 3SY7A 3T20A 2R4LA 3DZMA 1BH3A 2FGRA 2KZ7A 4G76A 5DL8A 3SYSA 3UU2A 3KVDD 2IWVA 3C5OA 3POUA 3VE1A 3AAAB 4FMSA 7PRNA 2M07A 4E1SA 2J4UP 3GP6A 4AFKA 2R4PA 2PRNA 2XE1A 2XTRA 3POXA 1OPFA 4GCSA 3A2SX 4C69X 1HXTA 2XTQA 3VZUX 3LK42 1QJPA 5AFUK 5JDPA 2R4NA 1S5LO 3DWNA 2WVPA 3NSGA 4RJXA 5DL6A 3WI4A 2GE4A 2MHLA 1G90A 3BS0A 5FVNA 4AKRA 1BXWA 2KZ7B 4GF4A 1PRNA 1H6S1 2J1NA 3VZWX 3FYXA 6PRNA 4F4BA 3AA1B 3AAAA 3AA7A 3AA0B 4LSIA 3VY8X 2XG6A 2O4VA 3VZTX 4K3BA 5H2FO 2W80C 4D64A 2XE2A 2QTKA 4N75A 4O3XB 3VE2A 2KC0A 5D5DA 4G75A 2N2MA 2OMFA 4GCPA 4PUXA 8PRNA 4XNLA 3AA6B 2Y0HA 3K19A 4D65A 3V8UA 4JFBA 1MM5A 1QJ9A 2ZFGA 5G38A 4AYMC 5IYUA 2R8AA 3LK41 4FUVA 2Y0KA 2K4TA 3EMNX 2WJRA 4U9CA 2W81C 5B5EO 4K3CA 3PRNA 3PGRA 4B61A 4AYID 5ADXL 4AKRB 4FZNA 4AYNA 4JCHA 5G26A 2XE5A 4FOZA 4FQEA 3T0SA 3O0EA 2F1VA 2KXPA 3HWBA 2IWWA 1GFNA 1T16A 3QRAA 3HOLA 2R4OA 2YPVA 4RLBA 2Y0LA 4RL9A 1ORMA 3SYBA 4AKMA 3DA3A 5GV0A 4FZLA 4O49A 4KRAA 3VY9X 3KZIO 4AUIA 1OSMA 1GFPA 2LFUA 3AA0A 3AA7B 5KAFO 5B66O 2JQYA 3PGSA 3NJTA 4XNKA 2MNHA 4AYEC 1QJ8A 2AXTO 4O3YA 3WU2O 5EE2A 4FZMA 3UPGA 5PRNA 4RJWA 4O4UA 2Y7SA 4O3ZA 1HXXA 4FESA 4N59A 1ZHZA 4QQ1A 3A0BO 2KXPB 4C4VB 2JMMA 2ERVA 2F1TA 1THQA
chains in the Genus database with same CATH topology
5T5FA 3HOEA 1ZHTA 4GHBA 4N58A 4O3WA 3T24A 3TZGA 5AFUL 1IZNB 2Y2XA 3WI5A 1YS5A 3QRCA 5DL7A 3UAQA 4D5UA 3HW9A 4KR8A 1ZHWA 3LK2A 4Z3TA 1ZHYA 2X27X 1BT9A 1E54A 4LSFA 3POQA 2ODJA 3AAEB 3DA4A 1GFQA 1MM4A 2M06A 4GCQA 2LHFA 3PORA 3SY9A 2XMXA 4LSEA 3LK3A 3AA1A 2YNKA 4LSHA 2FGQX 4FRXA 1HXUA 2K0LA 4FSOA 2ZLDA 3RBHA 3AAEA 1Q9FA 2N2LA 2PORA 1GFMA 1IZNA 4RLCA 4O4XA 5ADXK 3LK2B 1MPFA 1ZHXA 2XE3A 3PQUA 4FSPA 3SZVA 4AZLA 3PQSA 1P4TA 1PHOA 2KDYA 3JTYA 1GFOA 4BUMX 5DL5A 4FRTA 3SZDA 4KR4A 3AA6A 3LK3B 4FT6A 4AYDC 1Q9GA 3G7GA 4E1TA 3SY7A 3T20A 3SYSA 1BH3A 2FGRA 2KZ7A 4G76A 5DL8A 3UU2A 3VE1A 3KVDD 3C5OA 3POUA 3AAAB 4FMSA 7PRNA 2M07A 4E1SA 2J4UP 3GP6A 4AFKA 2XE1A 2PRNA 2XTRA 3POXA 1OPFA 4GCSA 3A2SX 4C69X 1HXTA 2XTQA 3VZUX 3LK42 1QJPA 5AFUK 5JDPA 3NSGA 3WI4A 4RJXA 5DL6A 1G90A 2GE4A 2MHLA 4AKRA 5FVNA 1BXWA 2KZ7B 4GF4A 1PRNA 1H6S1 2J1NA 3VZWX 3FYXA 6PRNA 4F4BA 3AA1B 3AAAA 3AA7A 3AA0B 4LSIA 3VY8X 2XG6A 2O4VA 3VZTX 2W80C 4D64A 2XE2A 2QTKA 4O3XB 3VE2A 2KC0A 5D5DA 4G75A 2N2MA 2OMFA 4GCPA 4PUXA 8PRNA 4XNLA 3AA6B 2Y0HA 3K19A 4D65A 3V8UA 4JFBA 1MM5A 1QJ9A 2ZFGA 4AYMC 3LK41 4FUVA 2Y0KA 2K4TA 3EMNX 4U9CA 2W81C 3PRNA 4B61A 4AYID 5ADXL 4AKRB 4FZNA 4AYNA 4JCHA 5G26A 2XE5A 4FOZA 3T0SA 3O0EA 2F1VA 2KXPA 3HWBA 1GFNA 3QRAA 3HOLA 2YPVA 4RLBA 2Y0LA 4RL9A 1ORMA 3SYBA 4AKMA 3DA3A 5GV0A 4FZLA 4O49A 4KRAA 3VY9X 4AUIA 1OSMA 1GFPA 2LFUA 3AA0A 3AA7B 4XNKA 2MNHA 4AYEC 1QJ8A 4O3YA 5EE2A 4FZMA 3UPGA 5PRNA 4RJWA 4O4UA 2Y7SA 4O3ZA 1HXXA 4FESA 4N59A 1ZHZA 4QQ1A 2KXPB 5IYUA 2JMMA 2ERVA 2F1TA 1THQA
chains in the Genus database with same CATH homology


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