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The Open Protein Structure Annotation Network
PDB Keyword
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3lhi

    Table of contents
        1. 1.1.1. Protein Summary
    1. 2. Summary
        1. 2.1.1. Ligand Summary

    Title Crystal structure of Putative 6-phosphogluconolactonase(YP_207848.1) from Neisseria gonorrhoeae FA 1090 at 1.33 A resolution. To be Published
    Site JCSG
    PDB Id 3lhi Target Id 398990
    Molecular Characteristics
    Source Neisseria gonorrhoeae fa 1090
    Alias Ids TPS30578,YP_207848.1, _0112.001592_ Molecular Weight 24876.64 Da.
    Residues 231 Isoelectric Point 5.10
    Sequence mfvwheyenaaeaaqsladavadalqgaldekggavlavsggrspiaffnalsqkdldwknvgitlade rivptnhadsntglvreyllknkaaaavwipmvedgktetelhpdavvdyalkhykqpdvlilgmgndg htasifpkapqfqtaidgsagvalvhttpvtapherismtldaiahtghvflaiqgeekkavfdqaaqg enreypislvlnhqgvnchvfyae
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.33 Rfree 0.161
    Matthews' coefficent 2.45 Rfactor 0.132
    Waters 394 Solvent Content 49.87

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3lhi

    Protein Summary

    Pfam update: This structure hits Glucosamine_iso PF01182, for which there are several known structures. The family has had its seed increased and been rebuilt since release 24, and Q5F8Q1 is now in the family.

    Gene NGO0716 from Neisseria gonorrhoeae fa 1090 encodes the YP_207848.1 protein, which is 96% identical to YP_001599435, a 6-phosphogluconolactonase. So far, it does not belong to any Pfam group. A temptative SCOP assignment is inside the alpha/beta class, NagB/RpiA/CoA transferase-like superfamily, NagB-like family.

     

     monomer.png

     

    Fig1. 3lhi is found as a monomer in the crystal structure.

     

    DALI search for structural similarity to 3lhi provides 1vl1 as top hit. The superposition of 3lhi with 1vl1 shows that overall structure is very similar. In the putative active site, 3lhi does not contain any ligand. However, a citric acid group (CIT) is found in the 1vl1 structure in contact with R43, H138, K190.

    super_1vl1.png

    Fig2. Superposition of 3lhi with the DALI top hit 1vl1.

     

    Dali summary is shown as below.

    Summary

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 1vl1-A 27.4 2.0 210 218 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 2: 1pbt-A 27.1 2.0 210 220 24 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 3: 3ico-C 27.1 2.2 220 247 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 4: 3ico-D 27.1 2.2 220 247 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 5: 3ico-A 26.9 2.2 219 244 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 6: 3ico-B 26.8 2.2 219 244 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 7: 3eb9-B 26.0 2.3 222 263 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 8: 3e7f-B 26.0 2.3 222 263 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 9: 3eb9-A 25.8 2.3 222 260 22 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 10: 3e7f-A 25.8 2.4 223 260 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 11: 2j0e-A 25.6 2.3 222 263 23 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 12: 2j0e-B 25.4 2.4 222 263 24 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 13: 3ch7-A 24.5 2.3 216 266 21 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 14: 3css-A 24.5 2.4 218 264 21 PDB MOLECULE: 6-PHOSPHOGLUCONOLACTONASE; 15: 1y89-A 24.2 2.3 210 238 23 PDB MOLECULE: DEVB PROTEIN; 16: 1y89-B 24.2 2.3 212 238 23 PDB MOLECULE: DEVB PROTEIN; 17: 2bkx-B 24.1 2.2 207 242 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 18: 2bkv-A 24.1 2.2 207 241 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 19: 2bkv-B 24.0 2.2 207 242 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 20: 2bkx-A 24.0 2.2 207 242 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 21: 3e15-A 23.8 2.3 217 291 20 PDB MOLECULE: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE; 22: 3e15-D 23.7 2.3 217 295 20 PDB MOLECULE: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE; 23: 3e15-C 23.6 2.4 218 295 20 PDB MOLECULE: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE; 24: 3e15-B 23.5 2.5 219 295 20 PDB MOLECULE: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE; 25: 1fs5-A 23.0 2.3 209 266 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 26: 3hn6-B 22.9 2.6 212 270 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 27: 2ri1-A 22.8 2.5 208 235 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 28: 1ne7-C 22.8 2.4 210 274 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE ISOMERASE; 29: 1ne7-D 22.8 2.4 210 274 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE ISOMERASE; 30: 1ne7-E 22.8 2.4 210 274 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE ISOMERASE; 31: 1ne7-F 22.8 2.4 210 274 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE ISOMERASE; 32: 1frz-A 22.8 2.3 209 266 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 33: 2wu1-A 22.8 2.3 210 266 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 34: 3hn6-A 22.8 2.6 211 271 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 35: 2ri1-B 22.8 2.5 208 235 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 36: 2ri0-A 22.8 2.5 208 234 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 37: 1hor-A 22.8 2.3 208 266 17 PDB MOLECULE: GLUCOSAMINE 6-PHOSPHATE DEAMINASE; 38: 1hot-A 22.8 2.3 208 266 17 PDB MOLECULE: GLUCOSAMINE 6-PHOSPHATE DEAMINASE; 39: 1hor-B 22.8 2.4 210 266 17 PDB MOLECULE: GLUCOSAMINE 6-PHOSPHATE DEAMINASE; 40: 1ne7-B 22.7 2.4 210 274 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE ISOMERASE; 41: 1fqo-B 22.7 2.4 210 266 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 42: 1frz-B 22.7 2.4 210 266 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 43: 1dea-A 22.7 2.3 208 266 17 PDB MOLECULE: GLUCOSAMINE 6-PHOSPHATE DEAMINASE; 44: 3hn6-D 22.7 2.7 211 270 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 45: 2ri0-B 22.7 2.5 208 234 16 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 46: 1hot-B 22.7 2.4 209 266 17 PDB MOLECULE: GLUCOSAMINE 6-PHOSPHATE DEAMINASE; 47: 1fqo-A 22.7 2.3 209 266 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 48: 1dea-B 22.7 2.4 209 266 17 PDB MOLECULE: GLUCOSAMINE 6-PHOSPHATE DEAMINASE; 49: 2wu1-B 22.6 2.4 210 266 17 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE DEAMINASE; 50: 1ne7-A 22.5 2.3 208 281 18 PDB MOLECULE: GLUCOSAMINE-6-PHOSPHATE ISOMERASE;

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

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     monomer.png
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    169.04 kB07:46, 21 Nov 2009gyewonActions
     super_1vl1.png
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    218.18 kB07:46, 21 Nov 2009gyewonActions
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