Structure of PDB 8bz7 Chain D Binding Site BS01

Receptor Information

>8bz7 Chain D (length=599) Species: 1639 (Listeria monocytogenes)

KDIKISVVVPTYNTELEGLKNLMASIDKQTMNPDEYELVFVDDGSTTDTY
ERLQEFAETRPNMTVKQIENSGWGSRPRNIATKMAKGEYILYLDHDDTVF
PETFERVYNFGKENNLDVVSGKEVRTNGWSWGWKQFSENNPHAEEMGIEC
LLPMTPHKFYKREFLLENDITFDDGARVLWEDVYFNSKAFIHGAKVGILA
DYPTYYWIATGRDPHEKWNQINKLFNFFKDNIKEQRDLDFMLTHWYRSRV
LGILGQWLLKNNNERIDIEFNYAKKLAEELIPAYISENLDKNNQVKDYLL
RQGDLDSLKKLAQIDAGITALSYVEDAYFKEDKLFFKTSTKMTYEDKEDF
FIEKTADRMERILPEEIKSKLPKEFFDYSDDLAEFTYEPSIKGRNSRATW
KIDGSTSNVEVVNKKANLYKIEGEMSFSVQINDYILDAADKKQPWDIATR
FTGLGYTSHRALTIGKILIKTALINNKTMIVYKNASGLISLDVGSSVRSI
VEDSGVKREQILIDKTSGKVTIPLNEIHVFGESLIEGNAELKPVGISDAD
PINVKAKLIGEANKARVEVLLGDEKLSGEYHLVTNIQGKKDKQQIKITL

Ligand information

• Ligand ID: TRH
• InChI: InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15+/m0/s1
• InChIKey: ZOSQFDVXNQFKBY-CGAXJHMRSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: C[C@@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
• Formula: C16 H26 N2 O15 P2
• Name: 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
• DrugBank: DB03723
• ZINC: ZINC000008218444
• PDB chain: 8bz7 Chain D Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bz7 Crystal structure of the L. monocytogenes RmlT in complex with TDP-rhamnose
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): P26 Y28 D59 G88 W89 G90 D110 H111 D112 P172 D198 W223
• Binding residue (residue number reindexed from 1): P10 Y12 D43 G72 W73 G74 D94 H95 D96 P156 D182 W207
• Annotation score: 4

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:8bz7, PDBe:8bz7, PDBj:8bz7
• PDBsum: 8bz7
• UniProt: A0A401AAP7