Structure of PDB 5wkg Chain A Binding Site BS01

Receptor Information

>5wkg Chain A (length=280) Species: 9606 (Homo sapiens)

FQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPW
SKGNFSDKEVAELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCE
LHSGGAIVSFLRGALGGLDFLSVKNASCVPSPEGGSRAQKFCALIIQYQG
IMETVRILLYETCPRYLLGVLNAGKADLQRQVKPEAWLSSGPSPGPGRLQ
LVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANWTWYLRATLDVAD
GEAAGLSCRVKHSSLEGQDIILYWRGSGLN

Ligand information

• Ligand ID: D21
• InChI: InChI=1S/C37H71O8P/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-37(39)45-35(34-44-46(40,41)42)33-43-36(38)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h17-18,35H,3-16,19-34H2,1-2H3,(H2,40,41,42)/t35-/m1/s1
• InChIKey: OPVZUEPSMJNLOM-PGUFJCEWSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)O)OC(=O)CCCCCCCC=CCCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P](O)(O)=O)OC(=O)CCCCCCC\C=C/CCCCCCCC
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCCC=CCCCCCCCC
  ACDLabs 12.01: CCCCCCCCCCCCCCCC(=O)OCC(COP(O)(O)=O)OC(=O)CCCCCCC\C=C/CCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(O)=O)OC(=O)CCCCCCCC=CCCCCCCCC
• Formula: C37 H71 O8 P
• Name: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
• PDB chain: 5wkg Chain A Residue 411

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wkg A molecular basis of human T cell receptor autoreactivity toward self-phospholipids.
• Resolution: 2.06 Å
• Binding residue (original residue number in PDB): F10 I69 Y73 F77 A100 V126 A129 C131 I148 M155 T157 V158 Y169
• Binding residue (residue number reindexed from 1): F7 I66 Y70 F74 A97 V123 A126 C128 I145 M152 T154 V155 Y166
• Annotation score: 1

External links

• PDB: RCSB:5wkg, PDBe:5wkg, PDBj:5wkg
• PDBsum: 5wkg
• PubMed: 29054999
• UniProt: P29016|CD1B_HUMAN T-cell surface glycoprotein CD1b (Gene Name=CD1B)