HEADER IMMUNE SYSTEM 15-MAR-22 7X9Q TITLE CRYSTAL STRUCTURE OF HUMAN STING COMPLEXED WITH COMPOUND BSP16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STIMULATOR OF INTERFERON GENES PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSTING,ENDOPLASMIC RETICULUM INTERFERON STIMULATOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: STING1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS STING AGONISTS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.PAN,X.GUAN,X.FENG,Z.LI,J.BIAN REVDAT 3 29-NOV-23 7X9Q 1 REMARK REVDAT 2 07-DEC-22 7X9Q 1 JRNL REVDAT 1 28-SEP-22 7X9Q 0 JRNL AUTH X.FENG,L.PAN,Z.QIAN,D.LIU,X.GUAN,L.FENG,B.SONG,X.XU,N.TAN, JRNL AUTH 2 Y.MA,Z.LI,Z.WANG,J.BIAN JRNL TITL DISCOVERY OF SELENIUM-CONTAINING STING AGONISTS AS ORALLY JRNL TITL 2 AVAILABLE ANTITUMOR AGENTS. JRNL REF J.MED.CHEM. V. 65 15048 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36069713 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00634 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 12879 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.450 REMARK 3 FREE R VALUE TEST SET COUNT : 702 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.0800 - 4.1000 0.90 2414 116 0.1750 0.2095 REMARK 3 2 4.1000 - 3.2600 0.88 2354 125 0.2125 0.2897 REMARK 3 3 3.2600 - 2.8500 0.93 2452 170 0.2545 0.2984 REMARK 3 4 2.8500 - 2.5900 0.94 2449 164 0.2708 0.3651 REMARK 3 5 2.5800 - 2.4000 0.95 2508 127 0.3116 0.3301 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7X9Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12879 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 47.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.64400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6UKM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, PH 7.5, EVAPORATION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 9.37843 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.25100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.42469 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 9.37843 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.25100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 50.42469 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 150 REMARK 465 GLY A 151 REMARK 465 ASN A 152 REMARK 465 ASN A 188 REMARK 465 TYR A 274 REMARK 465 SER A 275 REMARK 465 GLN A 276 REMARK 465 ALA A 277 REMARK 465 GLY A 278 REMARK 465 SER A 322 REMARK 465 PHE A 323 REMARK 465 GLU A 340 REMARK 465 VAL A 341 REMARK 465 THR A 342 REMARK 465 VAL A 343 REMARK 465 GLY A 344 REMARK 465 SER A 345 REMARK 465 LEU A 346 REMARK 465 LYS A 347 REMARK 465 THR A 348 REMARK 465 SER A 349 REMARK 465 ALA A 350 REMARK 465 VAL A 351 REMARK 465 PRO A 352 REMARK 465 SER A 353 REMARK 465 THR A 354 REMARK 465 SER A 355 REMARK 465 THR A 356 REMARK 465 MET A 357 REMARK 465 SER A 358 REMARK 465 GLN A 359 REMARK 465 GLU A 360 REMARK 465 PRO A 361 REMARK 465 GLU A 362 REMARK 465 LEU A 363 REMARK 465 LEU A 364 REMARK 465 ILE A 365 REMARK 465 SER A 366 REMARK 465 GLY A 367 REMARK 465 MET A 368 REMARK 465 GLU A 369 REMARK 465 LYS A 370 REMARK 465 PRO A 371 REMARK 465 LEU A 372 REMARK 465 PRO A 373 REMARK 465 LEU A 374 REMARK 465 ARG A 375 REMARK 465 THR A 376 REMARK 465 ASP A 377 REMARK 465 PHE A 378 REMARK 465 SER A 379 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 153 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 180 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 184 CG CD OE1 NE2 REMARK 470 ASN A 187 CG OD1 ND2 REMARK 470 LEU A 190 CG CD1 CD2 REMARK 470 ARG A 191 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 196 CG CD OE1 NE2 REMARK 470 ASP A 216 CG OD1 OD2 REMARK 470 PHE A 279 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 281 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 316 CG CD OE1 OE2 REMARK 470 ASP A 319 CG OD1 OD2 REMARK 470 ASP A 320 CG OD1 OD2 REMARK 470 ARG A 331 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 335 CG CD OE1 NE2 REMARK 470 GLU A 337 CG CD OE1 OE2 REMARK 470 GLU A 339 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 167 -63.90 -139.96 REMARK 500 GLN A 184 -72.18 -89.65 REMARK 500 GLN A 196 29.44 -79.97 REMARK 500 ASN A 211 -149.65 -154.00 REMARK 500 ALA A 215 76.84 24.06 REMARK 500 ASP A 216 88.41 -166.90 REMARK 500 PRO A 217 -27.77 -38.97 REMARK 500 HIS A 232 114.64 -162.57 REMARK 500 ASN A 307 51.23 30.54 REMARK 500 REMARK 500 REMARK: NULL DBREF 7X9Q A 150 379 UNP Q86WV6 STING_HUMAN 150 379 SEQRES 1 A 230 LYS GLY ASN PHE ASN VAL ALA HIS GLY LEU ALA TRP SER SEQRES 2 A 230 TYR TYR ILE GLY TYR LEU ARG LEU ILE LEU PRO GLU LEU SEQRES 3 A 230 GLN ALA ARG ILE ARG THR TYR ASN GLN HIS TYR ASN ASN SEQRES 4 A 230 LEU LEU ARG GLY ALA VAL SER GLN ARG LEU TYR ILE LEU SEQRES 5 A 230 LEU PRO LEU ASP CYS GLY VAL PRO ASP ASN LEU SER MET SEQRES 6 A 230 ALA ASP PRO ASN ILE ARG PHE LEU ASP LYS LEU PRO GLN SEQRES 7 A 230 GLN THR GLY ASP HIS ALA GLY ILE LYS ASP ARG VAL TYR SEQRES 8 A 230 SER ASN SER ILE TYR GLU LEU LEU GLU ASN GLY GLN ARG SEQRES 9 A 230 ALA GLY THR CYS VAL LEU GLU TYR ALA THR PRO LEU GLN SEQRES 10 A 230 THR LEU PHE ALA MET SER GLN TYR SER GLN ALA GLY PHE SEQRES 11 A 230 SER ARG GLU ASP ARG LEU GLU GLN ALA LYS LEU PHE CYS SEQRES 12 A 230 ARG THR LEU GLU ASP ILE LEU ALA ASP ALA PRO GLU SER SEQRES 13 A 230 GLN ASN ASN CYS ARG LEU ILE ALA TYR GLN GLU PRO ALA SEQRES 14 A 230 ASP ASP SER SER PHE SER LEU SER GLN GLU VAL LEU ARG SEQRES 15 A 230 HIS LEU ARG GLN GLU GLU LYS GLU GLU VAL THR VAL GLY SEQRES 16 A 230 SER LEU LYS THR SER ALA VAL PRO SER THR SER THR MET SEQRES 17 A 230 SER GLN GLU PRO GLU LEU LEU ILE SER GLY MET GLU LYS SEQRES 18 A 230 PRO LEU PRO LEU ARG THR ASP PHE SER HET A9X A 401 22 HETNAM A9X (2R)-4-(5,6-DIMETHOXY-1-BENZOSELENOPHEN-2-YL)-2-ETHYL- HETNAM 2 A9X 4-OXIDANYLIDENE-BUTANOIC ACID FORMUL 2 A9X C16 H18 O5 SE FORMUL 3 HOH *4(H2 O) HELIX 1 AA1 PHE A 153 TYR A 167 1 15 HELIX 2 AA2 TYR A 167 TYR A 186 1 20 HELIX 3 AA3 THR A 263 MET A 271 1 9 HELIX 4 AA4 SER A 280 ALA A 302 1 23 HELIX 5 AA5 LEU A 325 LYS A 338 1 14 SHEET 1 AA1 5 ILE A 219 LYS A 224 0 SHEET 2 AA1 5 SER A 243 GLU A 249 -1 O ILE A 244 N ASP A 223 SHEET 3 AA1 5 GLN A 252 TYR A 261 -1 O ALA A 254 N LEU A 247 SHEET 4 AA1 5 LEU A 198 PRO A 203 1 N LEU A 201 O GLU A 260 SHEET 5 AA1 5 CYS A 309 TYR A 314 1 O ILE A 312 N LEU A 202 SHEET 1 AA2 2 GLN A 228 HIS A 232 0 SHEET 2 AA2 2 ILE A 235 TYR A 240 -1 O TYR A 240 N GLN A 228 CRYST1 33.649 54.502 101.943 90.00 98.40 90.00 I 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029719 0.000000 0.004391 0.00000 SCALE2 0.000000 0.018348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009916 0.00000