Structure of PDB 7f2a Chain A Binding Site BS01

Receptor Information

>7f2a Chain A (length=376) Species: 487 (Neisseria meningitidis)

PPFVCWIFCKVIDNFGDIGVSWRLARVLHRELGWQVHLWTDDVSALRALC
PDLPDVPCVHQDIHVRTWHSDAADIDTAPVPDVVIGTFACDLPENVLHII
RRHKPLWLNWEYLSAEESNERLHLMPSPQEGVQKYFWFMGFSEKSGGLIR
ERDYCEAVRFDSEALRQRLMLPEKNAPEWLLFGYRSDVWAKWLEMWRQAG
SPMTLLLAGTQIIDSLKQSGVIPQDALQNDGDVFQTASVRLVKIPFVPQQ
DFDKLLHLADCAVIRGEDSFVRAQLAGKPFFWHIYPQDENVHLDKLHAFW
DKAHGFYTPETVSAHRRLSDDLNGGGALSATQRLECWQILQQHQNGWRQG
AEDWSRYLFGQPSASEKLAAFVSKHQ

Ligand information

• Ligand ID: TYD
• InChI: InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
• InChIKey: UJLXYODCHAELLY-XLPZGREQSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
• Formula: C10 H16 N2 O11 P2
• Name: THYMIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL259724
• DrugBank: DB03103
• ZINC: ZINC000008215882
• PDB chain: 7f2a Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7f2a Crystal structure of Neisseria meningitidis EarP bound TDP
• Resolution: 2.58 Å
• Binding residue (original residue number in PDB): N17 F18 G19 L52 F185 Y187 F249 V250 Q252 F255 R268 E270 D271 S272
• Binding residue (residue number reindexed from 1): N14 F15 G16 L49 F182 Y184 F246 V247 Q249 F252 R265 E267 D268 S269
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0016757 glycosyltransferase activity
• GO:0106361 protein-arginine rhamnosyltransferase activity

External links

• PDB: RCSB:7f2a, PDBe:7f2a, PDBj:7f2a
• PDBsum: 7f2a
• UniProt: X5EQ00