3RYBA

Lactococcal oppa complexed with slsqslsqs
Total Genus 203
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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
203
sequence length
563
structure length
563
Chain Sequence
KLKAGNFDVAYQNPDKAIKGGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGSDRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSITYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSVKGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNFGHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGVSSAKL
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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.

publication title Importance of a Hydrophobic Pocket for Peptide Binding in Lactococcal OppA.
pubmed doi rcsb
molecule tags Peptide binding protein
source organism Lactococcus lactis
molecule keywords Oligopeptide-binding protein oppA
total genus 203
structure length 563
sequence length 563
ec nomenclature
pdb deposition date 2011-05-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00496 SBP_bac_5 Bacterial extracellular solute-binding proteins, family 5 Middle
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.10.105.10 Alpha Beta Roll Dipeptide-binding Protein; domain 3 Dipeptide-binding Protein; Domain 3 3rybA02
1DPEA 4QFPA 3DRIA 3ZS6A 3O9PA 4PFWA 1JEUA 4QFLA 1B3FA 1VR5A 1B3LA 3MVXA 4XKQA 1B7HA 1DPPA 4ZEBA 3TCHA 1JETA 4OFLA 2Z23A 5KZTA 4OESA 1UIVA 3TCFA 3O6PA 1XOCA 1B9JA 3MVYA 2B4LA 4JSDA 4ZE8A 5L8DA 3DRJA 2O7IA 2WOLA 1B1HA 3TPAA 1QKBA 4XKPA 1B52A 1OLAA 3RYBA 4TOZA 3PAMA 1B3GA 4ZECA 2NOOA 3MVWA 4GFRA 4GF8A 3LVUA 4ZEDA 1RKMA 4OFOA 5F1QA 3DRKA 1UQWA 2OLBA 4RA1A 4OEVA 3MW0A 3QIMA 4ZEIA 4OETA 3MVZA 3CHGA 4PFTA 1B5JA 3MZ9A 4WEDA 3DP8A 4I9DA 4ONYA 3RQTA 4DCXA 4OERA 2WOKA 4QFKA 1ZTYA 4ZE9A 1B58A 4XKRA 3TCGA 2WOPA 3T66A 4OEUA 4QFOA 4JSOA 4XKNA 1B32A 4ZEKA 1ZU0A 4PFYA 4FAJA 4I8CA 3DRFA 5HM4B 4PFUA 1B4HA 1OLCA 1B05A 4DCYA 1B2HA 2GRVA 1B0HA 5ICQA 1B3HA 1UIUA 1B51A 4GL8A 1QKAA 3M8UA 5ISUA 3MZBA 3RY3A 4OFJA 3I5OA 1B4ZA 1B40A 2B4MA 1B5HA 1B5IA 1B6HA 2RKMA 3RYAA 1B46A 3E3KA 3DRHA 3FTOA 4QFNA 1JEVA 3DRGA 2D5WA 1ZLQA
chains in the Genus database with same CATH superfamily
1DPEA 4QFPA 3DRIA 3ZS6A 3O9PA 4PFWA 1JEUA 4QFLA 1B3FA 1VR5A 1B3LA 3MVXA 4XKQA 1B7HA 1DPPA 4ZEBA 3TCHA 1JETA 4OFLA 2Z23A 5KZTA 4OESA 1UIVA 3TCFA 3O6PA 1XOCA 1B9JA 3MVYA 2B4LA 4JSDA 4ZE8A 5L8DA 3DRJA 2O7IA 2WOLA 1B1HA 3TPAA 1QKBA 4XKPA 1B52A 1OLAA 3RYBA 4TOZA 3PAMA 1B3GA 4ZECA 2NOOA 3MVWA 4GFRA 4GF8A 3LVUA 4ZEDA 1RKMA 4OFOA 5F1QA 3DRKA 1UQWA 2OLBA 4RA1A 4OEVA 3MW0A 3QIMA 4ZEIA 4OETA 3MVZA 3CHGA 4PFTA 1B5JA 3MZ9A 4WEDA 3DP8A 4I9DA 4ONYA 3RQTA 4DCXA 4OERA 2WOKA 4QFKA 1ZTYA 4ZE9A 1B58A 4XKRA 3TCGA 2WOPA 3T66A 4OEUA 4QFOA 4JSOA 4XKNA 1B32A 4ZEKA 1ZU0A 4PFYA 4FAJA 4I8CA 3DRFA 5HM4B 4PFUA 1B4HA 1OLCA 1B05A 4DCYA 1B2HA 2GRVA 1B0HA 5ICQA 1B3HA 1UIUA 1B51A 4GL8A 1QKAA 3M8UA 5ISUA 3MZBA 3RY3A 4OFJA 3I5OA 1B4ZA 1B40A 2B4MA 1B5HA 1B5IA 1B6HA 2RKMA 3RYAA 1B46A 3E3KA 3DRHA 3FTOA 4QFNA 1JEVA 3DRGA 2D5WA 1ZLQA
chains in the Genus database with same CATH topology
1DPEA 4QFPA 3DRIA 3ZS6A 3O9PA 4PFWA 1JEUA 4QFLA 1B3FA 1VR5A 1B3LA 3MVXA 4XKQA 1B7HA 1DPPA 4ZEBA 3TCHA 1JETA 4OFLA 2Z23A 5KZTA 4OESA 1UIVA 3TCFA 3O6PA 1XOCA 1B9JA 3MVYA 2B4LA 4JSDA 4ZE8A 5L8DA 3DRJA 2O7IA 2WOLA 1B1HA 3TPAA 1QKBA 4XKPA 1B52A 1OLAA 3RYBA 4TOZA 3PAMA 1B3GA 4ZECA 2NOOA 3MVWA 4GFRA 4GF8A 3LVUA 4ZEDA 1RKMA 4OFOA 5F1QA 3DRKA 1UQWA 2OLBA 4RA1A 4OEVA 3MW0A 3QIMA 4ZEIA 4OETA 3MVZA 3CHGA 4PFTA 1B5JA 3MZ9A 4WEDA 3DP8A 4I9DA 4ONYA 3RQTA 4DCXA 4OERA 2WOKA 4QFKA 1ZTYA 4ZE9A 1B58A 4XKRA 3TCGA 2WOPA 3T66A 4OEUA 4QFOA 4JSOA 4XKNA 1B32A 4ZEKA 1ZU0A 4PFYA 4FAJA 4I8CA 3DRFA 5HM4B 4PFUA 1B4HA 1OLCA 1B05A 4DCYA 1B2HA 2GRVA 1B0HA 5ICQA 1B3HA 1UIUA 1B51A 4GL8A 1QKAA 3M8UA 5ISUA 3MZBA 3RY3A 4OFJA 3I5OA 1B4ZA 1B40A 2B4MA 1B5HA 1B5IA 1B6HA 2RKMA 3RYAA 1B46A 3E3KA 3DRHA 3FTOA 4QFNA 1JEVA 3DRGA 2D5WA 1ZLQA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1DPE A;  4QFP A;  3DRI A;  3ZS6 A;  3O9P A;  4PFW A;  1JEU A;  4QFL A;  1B3F A;  1VR5 A;  1B3L A;  3MVX A;  4XKQ A;  1B7H A;  1DPP A;  4ZEB A;  3TCH A;  1JET A;  4OFL A;  2Z23 A;  5KZT A;  4OES A;  1UIV A;  3TCF A;  3O6P A;  1XOC A;  1B9J A;  3MVY A;  2B4L A;  4JSD A;  4ZE8 A;  5L8D A;  3DRJ A;  2O7I A;  2WOL A;  1B1H A;  3TPA A;  1QKB A;  4XKP A;  1B52 A;  1OLA A;  3RYB A;  4TOZ A;  3PAM A;  1B3G A;  4ZEC A;  2NOO A;  3MVW A;  4GFR A;  4GF8 A;  3LVU A;  4ZED A;  1RKM A;  4OFO A;  5F1Q A;  3DRK A;  1UQW A;  2OLB A;  4RA1 A;  4OEV A;  3MW0 A;  3QIM A;  4ZEI A;  4OET A;  3MVZ A;  3CHG A;  4PFT A;  1B5J A;  3MZ9 A;  4WED A;  3DP8 A;  4I9D A;  4ONY A;  3RQT A;  4DCX A;  4OER A;  2WOK A;  4QFK A;  1ZTY A;  4ZE9 A;  1B58 A;  4XKR A;  3TCG A;  2WOP A;  3T66 A;  4OEU A;  4QFO A;  4JSO A;  4XKN A;  1B32 A;  4ZEK A;  1ZU0 A;  4PFY A;  4FAJ A;  4I8C A;  3DRF A;  5HM4 B;  4PFU A;  1B4H A;  1OLC A;  1B05 A;  4DCY A;  1B2H A;  2GRV A;  1B0H A;  5ICQ A;  1B3H A;  1UIU A;  1B51 A;  4GL8 A;  1QKA A;  3M8U A;  5ISU A;  3MZB A;  3RY3 A;  4OFJ A;  3I5O A;  1B4Z A;  1B40 A;  2B4M A;  1B5H A;  1B5I A;  1B6H A;  2RKM A;  3RYA A;  1B46 A;  3E3K A;  3DRH A;  3FTO A;  4QFN A;  1JEV A;  3DRG A;  2D5W A;  1ZLQ A; 
#chains in the Genus database with same CATH topology
 1DPE A;  4QFP A;  3DRI A;  3ZS6 A;  3O9P A;  4PFW A;  1JEU A;  4QFL A;  1B3F A;  1VR5 A;  1B3L A;  3MVX A;  4XKQ A;  1B7H A;  1DPP A;  4ZEB A;  3TCH A;  1JET A;  4OFL A;  2Z23 A;  5KZT A;  4OES A;  1UIV A;  3TCF A;  3O6P A;  1XOC A;  1B9J A;  3MVY A;  2B4L A;  4JSD A;  4ZE8 A;  5L8D A;  3DRJ A;  2O7I A;  2WOL A;  1B1H A;  3TPA A;  1QKB A;  4XKP A;  1B52 A;  1OLA A;  3RYB A;  4TOZ A;  3PAM A;  1B3G A;  4ZEC A;  2NOO A;  3MVW A;  4GFR A;  4GF8 A;  3LVU A;  4ZED A;  1RKM A;  4OFO A;  5F1Q A;  3DRK A;  1UQW A;  2OLB A;  4RA1 A;  4OEV A;  3MW0 A;  3QIM A;  4ZEI A;  4OET A;  3MVZ A;  3CHG A;  4PFT A;  1B5J A;  3MZ9 A;  4WED A;  3DP8 A;  4I9D A;  4ONY A;  3RQT A;  4DCX A;  4OER A;  2WOK A;  4QFK A;  1ZTY A;  4ZE9 A;  1B58 A;  4XKR A;  3TCG A;  2WOP A;  3T66 A;  4OEU A;  4QFO A;  4JSO A;  4XKN A;  1B32 A;  4ZEK A;  1ZU0 A;  4PFY A;  4FAJ A;  4I8C A;  3DRF A;  5HM4 B;  4PFU A;  1B4H A;  1OLC A;  1B05 A;  4DCY A;  1B2H A;  2GRV A;  1B0H A;  5ICQ A;  1B3H A;  1UIU A;  1B51 A;  4GL8 A;  1QKA A;  3M8U A;  5ISU A;  3MZB A;  3RY3 A;  4OFJ A;  3I5O A;  1B4Z A;  1B40 A;  2B4M A;  1B5H A;  1B5I A;  1B6H A;  2RKM A;  3RYA A;  1B46 A;  3E3K A;  3DRH A;  3FTO A;  4QFN A;  1JEV A;  3DRG A;  2D5W A;  1ZLQ A; 
#chains in the Genus database with same CATH homology
 1DPE A;  4QFP A;  3DRI A;  3ZS6 A;  3O9P A;  4PFW A;  1JEU A;  4QFL A;  1B3F A;  1VR5 A;  1B3L A;  3MVX A;  4XKQ A;  1B7H A;  1DPP A;  4ZEB A;  3TCH A;  1JET A;  4OFL A;  2Z23 A;  5KZT A;  4OES A;  1UIV A;  3TCF A;  3O6P A;  1XOC A;  1B9J A;  3MVY A;  2B4L A;  4JSD A;  4ZE8 A;  5L8D A;  3DRJ A;  2O7I A;  2WOL A;  1B1H A;  3TPA A;  1QKB A;  4XKP A;  1B52 A;  1OLA A;  3RYB A;  4TOZ A;  3PAM A;  1B3G A;  4ZEC A;  2NOO A;  3MVW A;  4GFR A;  4GF8 A;  3LVU A;  4ZED A;  1RKM A;  4OFO A;  5F1Q A;  3DRK A;  1UQW A;  2OLB A;  4RA1 A;  4OEV A;  3MW0 A;  3QIM A;  4ZEI A;  4OET A;  3MVZ A;  3CHG A;  4PFT A;  1B5J A;  3MZ9 A;  4WED A;  3DP8 A;  4I9D A;  4ONY A;  3RQT A;  4DCX A;  4OER A;  2WOK A;  4QFK A;  1ZTY A;  4ZE9 A;  1B58 A;  4XKR A;  3TCG A;  2WOP A;  3T66 A;  4OEU A;  4QFO A;  4JSO A;  4XKN A;  1B32 A;  4ZEK A;  1ZU0 A;  4PFY A;  4FAJ A;  4I8C A;  3DRF A;  5HM4 B;  4PFU A;  1B4H A;  1OLC A;  1B05 A;  4DCY A;  1B2H A;  2GRV A;  1B0H A;  5ICQ A;  1B3H A;  1UIU A;  1B51 A;  4GL8 A;  1QKA A;  3M8U A;  5ISU A;  3MZB A;  3RY3 A;  4OFJ A;  3I5O A;  1B4Z A;  1B40 A;  2B4M A;  1B5H A;  1B5I A;  1B6H A;  2RKM A;  3RYA A;  1B46 A;  3E3K A;  3DRH A;  3FTO A;  4QFN A;  1JEV A;  3DRG A;  2D5W A;  1ZLQ 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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