Structure of PDB 6mss Chain A Binding Site BS01

Receptor Information

>6mss Chain A (length=181) Species: 10090 (Mus musculus)

MPVEQNPPALSLYEGADSGLRCNFSTTMKSVQWFQQNHRGRLITLFYLAQ
GTKENGRLKSTFNSKERYSTLHIKDAQLEDSGTYFCAAVNMGYKLTFGTG
TSLLVDPNIQNPDPAVYQLRDSKSKSVCLFTDFDSQTNVSQSSDVYITDK
CVLDMRSMDFKSNSAVAWSNKSDFACANAFN

Ligand information

• Ligand ID: SRV
• InChI: InChI=1S/C45H84O11/c1-4-6-8-10-12-13-14-15-16-17-18-19-25-29-33-39(47)55-37(35-54-45-42(50)40(48)41(49)43(56-45)44(51)52)34-53-38(46)32-28-24-21-20-23-27-31-36(3)30-26-22-11-9-7-5-2/h36-37,40-43,45,48-50H,4-35H2,1-3H3,(H,51,52)/t36-,37+,40-,41-,42+,43-,45-/m0/s1
• InChIKey: GTQHUJVSZUDBBM-ASILJYLZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCCCCCC(=O)OC(COC1C(C(C(C(O1)C(=O)O)O)O)O)COC(=O)CCCCCCCCC(C)CCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCCCCC(=O)O[CH](CO[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O)COC(=O)CCCCCCCC[CH](C)CCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O)COC(=O)CCCCCCCC[C@@H](C)CCCCCCCC
  ACDLabs 12.01: OC1C(O)C(O)C(OC1C(O)=O)OCC(COC(=O)CCCCCCCCC(CCCCCCCC)C)OC(=O)CCCCCCCCCCCCCCCC
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCCCCCC(=O)O[C@@H](CO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C(=O)O)O)O)O)COC(=O)CCCCCCCC[C@@H](C)CCCCCCCC
• Formula: C45 H84 O11
• Name: (2S)-2-(heptadecanoyloxy)-3-{[(10S)-10-methyloctadecanoyl]oxy}propyl alpha-D-glucopyranosiduronic acid
• PDB chain: 6mss Chain C Residue 405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6mss Distinct CD1d docking strategies exhibited by diverse Type II NKT cell receptors.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): T29 K31 K67
• Binding residue (residue number reindexed from 1): T27 K29 K65
• Annotation score: 1

External links

• PDB: RCSB:6mss, PDBe:6mss, PDBj:6mss
• PDBsum: 6mss
• PubMed: 31748533