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Establishing meaningful asymmetric unit

Explore the structural details of the monomeric and hexameric forms of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from Enterococcus faecalis using PDB entries 1YWK. Gain insights into the interchain interactions and analyze the protein's structural features in the asymmetric unit.

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Establishing meaningful asymmetric unit

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  1. Establishing meaningful asymmetric unit dimer 2 monomers What?

  2. 1YWK 4-DEOXY-1-THREO-5-HEXOSULOSE-URONATE KETOL-ISOMERASE ENTEROCOCCUS FAECALIS PDB – monomeric MSD -hexameric

  3. 1YWK PDB 6 monomers in the ASU

  4. http://pqs.ebi.ac.uk/pqs-quick.html

  5. 1YWK MSD – Hexamer in ASU 2 interchain salt bridges per chain 2221.7 Ang**2 ASA -16.66 kcal/mol

  6. http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

  7. MSLQNMETRYTHSPADIRHYSTEQLR DEFLVEKVFIPGAISLTYTHNDRMIF GGVTPTTEELEIILDKELGVDYFLER RELGVINIGGPGFIEIDGAKETMKKQ DGYYIGKETKHVRFSSENPDNPAKFY ISCVPAHHKYPNVKISIDEITPMETG DPLTLNQRKIYQYIHPNVCESCQLQM GYTILEPGSAWNTMPCHTHERRMEAY VYFDMEEDTRIFHMMGKPDETKHLVM SNEQAAISPSWSIHSGVGTSNYSFIW AMCGENITYTDMDMVAMDQLKEGHHHHHH CLONING ARTIFACT/IS TAG

  8. GLU 1260 ARG 1044 HIS 1132

  9. http://www.ebi.ac.uk/msd-srv/ssm/

  10. 1x8m, 1xru, 1sfn

  11. 1YWK + 1XRU

  12. 1XRU Hexameric

  13. 1YWK + 1SFN

  14. 1SFN Tetrameric ?

  15. 1SFN PDB Dimer in ASU ? Tetramer Tetramer

  16. 1SFN C-Terminus unobserved C-terminal GLY

  17. 4-DEOXY-L-THREO-5-HEXOSULOSE-URONATE KETOL-ISOMERASE 1 1YWK ENTEROCOCCUS FAECALIS SWS Q838L9 KDI1_ENTFA 1XRU ESCHERICHIA COLI SWS Q46938 KDUI_ECOLI 1X8M ESCHERICHIA COLI SWS Q46938 KDUI_ECOLI CONSERVED HYPOTHETICAL PROTEIN 1SFN DEINOCOCCUS RADIODURANS GB 15806172 NP_294876

  18. 1YWK 81.010 107.685 191.021 90.00 90.00 90.00 P 21 21 21 24 1XRU 102.972 102.972 176.862 90.00 90.00 120.00 H 3 18 1X8M 101.011 101.011 179.410 90.00 90.00 120.00 P 31 18 1SFN 109.370 109.370 95.408 90.00 90.00 90.00 P 4 21 2 16 1XRU and 1X8M same species different space group 1YWK Hexameric 1XRU Hexameric 1X8M Hexameric 1SFN Tetrameric

  19. http://www.ebi.ac.uk/msd-srv/MSDtemplate/

  20. 1ywk 1x8m 1xru PHE PRO PHE | PHE PRO PHE | PHE PRO PHE 1124 1052 1113 | 1128 1054 1117 | 126 52 115 SER SER SER | SER SER SER | SER SER SER 1237 1241 1239 | 1241 1245 1243 | 239 243 241 PHE ASP SER | PHE ASN PHE | PHE ASN PHE 1206 1207 1252 | 1208 1235 1032 | 206 233 30

  21. 1sfn ASP PHE LYS 1239 1050 1119 PHE ASP PHE 1163 1164 1165 PHE PHE PHE 1165 1117 1071 PHE PHE PRO 1165 1163 1130 PHE PHE SER 1117 1071 1115 PHE SER PHE 1073 1115 1117 SER SER PHE 1232 1171 1172

  22. PHE 1206 SER 1252 ASP 1207

  23. http://www.ebi.ac.uk/intenz/

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