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


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