Structure of PDB 3gg2 Chain D Binding Site BS02

Receptor Information

>3gg2 Chain D (length=427) Species: 837 (Porphyromonas gingivalis)

LDIAVVGIGYVGLVSATCFAELGANVRCIDTDRNKIEQLNSGTIPIYEPG
LEKMIARNVKAGRLRFGTEIEQAVPEADIIFIAVGTPGSADMSYVLDAAR
SIGRAMSRYILIVTKSTVPVGSYRLIRKAIQEELDKREVLIDFDIASNPE
FLKEGNAIDDFMKPDRVVVGVDSDRARELITSLYKPMLLNNFRVLFMDIA
SAEMTKYAANAMLATRISFMNDVANLCERVGADVSMVRLGIGSDSRIGSK
FLYPGCGYGGSCFPKDVKALIRTAEDNGYRMEVLEAVERVNEKQKSILFD
KFSTYYKGNVQGRCVAIWGLSFKPGTDDMREAPSLVLIEKLLEVGCRVRV
YDPVAMKEAQKRLGDKVEYTTDMYDAVRGAEALFHVTEWKEFRMPDWSAL
SQAMAASLVIDGRNVYELPDFTLLNIG

Ligand information

• Ligand ID: UGA
• InChI: InChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1
• InChIKey: HDYANYHVCAPMJV-LXQIFKJMSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C3OC(OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O)C(O)C(O)C3O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)O)O)O)O)O
  CACTVS 3.341: O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O
• Formula: C15 H22 N2 O18 P2
• Name: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID;
  UDP-GLUCURONIC ACID
• ChEMBL: CHEMBL228057
• DrugBank: DB03041
• ZINC: ZINC000008215691
• PDB chain: 3gg2 Chain D Residue 4000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gg2 Crystal structure of UDP-glucose 6-dehydrogenase from Porphyromonas gingivalis bound to product UDP-glucuronate
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F233 L234 K235 E236 K288 N292 I299 F333 Y335 Y340 G341 C344 F345 F404 K405
• Binding residue (residue number reindexed from 1): F151 L152 K153 E154 K206 N210 I217 F251 Y253 Y258 G259 C262 F263 F322 K323
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): T199 E236 K288 N292 C344 D348
• Catalytic site (residue number reindexed from 1): T117 E154 K206 N210 C262 D266
• Enzyme Commision number: 1.1.1.22: UDP-glucose 6-dehydrogenase.

Gene Ontology

Molecular Function

• GO:0003979 UDP-glucose 6-dehydrogenase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0051287 NAD binding

Biological Process

• GO:0000271 polysaccharide biosynthetic process

External links

• PDB: RCSB:3gg2, PDBe:3gg2, PDBj:3gg2
• PDBsum: 3gg2
• UniProt: Q7MVC7