Structure of PDB 8bz6 Chain C Binding Site BS01

Receptor Information

>8bz6 Chain C (length=606) Species: 1639 (Listeria monocytogenes)

DIKISVVVPTYNTELEGLKNLMASIDKQTMNPDEYELVFVDDGSTTDTYE
RLQEFAETRPNMTVKQIENSGWGSRPRNIATKMAKGEYILYLDHDDTVFP
ETFERVYNFGKENNLDVVSGKEVRTNGWSWGWKQFSENNPHAEEMGIECL
LPMTPHKFYKREFLLENDITFDDGARVLWEDVYFNSKAFIHGAKVGILAD
YPTYYWIATGANNSSSFGRDPHEKWNQINKLFNFFKDNIKEQRDLDFMLT
HWYRSRVLGILGQWLLKNNNERIDIEFNYAKKLAEELIPAYISENLDKNN
QVKDYLLRQGDLDSLKKLAQIDAGITALSYVEDAYFKEDKLFFKTSTKMT
YEDKEDFFIEKTADRMERILPEEIKSKLPKEFFDYSDDLAEFTYEPSIKG
RNSRATWKIDGSTSNVEVVNKKANLYKIEGEMSFSVQINDYILDAADKKQ
PWDIATRFTGLGYTSHRALTIGKILIKTALINNKTMIVYKNASGLISLDV
GSSVRSIVEDSGVKREQILIDKTSGKVTIPLNEIHVFGESLIEGNAELKP
VGISDADPINVKAKLIGEANKARVEVLLGDEKLSGEYHLVTNIQGKKDKQ
QIKITL

Ligand information

• Ligand ID: UPG
• InChI: InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1
• InChIKey: HSCJRCZFDFQWRP-JZMIEXBBSA-N
• SMILES:
  CACTVS 3.370: OC[C@H]1O[C@H](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)[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 12.01: O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O
  CACTVS 3.370: OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.7.6: 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)CO)O)O)O)O)O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
• Formula: C15 H24 N2 O17 P2
• Name: URIDINE-5'-DIPHOSPHATE-GLUCOSE;
  URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER
• ChEMBL: CHEMBL375951
• DrugBank: DB01861
• ZINC: ZINC000008215472
• PDB chain: 8bz6 Chain C Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bz6 Crystal structure of the L. monocytogenes RmlT in complex with UDP-glucose
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): P26 Y28 D59 G88 W89 D110 H111 D112 P172 H173 E197 W223 N229
• Binding residue (residue number reindexed from 1): P9 Y11 D42 G71 W72 D93 H94 D95 P155 H156 E180 W206 N212
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0016757 glycosyltransferase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:8bz6, PDBe:8bz6, PDBj:8bz6
• PDBsum: 8bz6
• UniProt: A0A401AAP7