HEADER SIGNALING PROTEIN 17-JAN-23 8C7W TITLE CRYSTAL STRUCTURE OF THE ACVR1 (ALK2) KINASE IN COMPLEX WITH THE TITLE 2 COMPOUND M4K2304 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACTIVIN RECEPTOR TYPE I; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.11.30; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ACVR1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS BMP SIGNALLING KINASE INHIBITOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.CROS,E.P.WILLIAMS,M.N.SWEENEY,D.SMIL,H.GONZALEZ-ALVAREZ,R.AL-AWAR, AUTHOR 2 A.N.BULLOCK REVDAT 2 07-FEB-24 8C7W 1 REMARK REVDAT 1 08-FEB-23 8C7W 0 JRNL AUTH J.CROS,E.P.WILLIAMS,M.N.SWEENEY,D.SMIL,H.GONZALEZ-ALVAREZ, JRNL AUTH 2 R.AL-AWAR,A.N.BULLOCK JRNL TITL CRYSTAL STRUCTURE OF THE ACVR1 (ALK2) KINASE IN COMPLEX WITH JRNL TITL 2 THE COMPOUND M4K2304 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 871 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 57.2000 - 4.1100 1.00 3004 145 0.1708 0.1833 REMARK 3 2 4.1000 - 3.2600 1.00 2856 162 0.1798 0.2089 REMARK 3 3 3.2600 - 2.8500 1.00 2828 138 0.2092 0.2724 REMARK 3 4 2.8500 - 2.5900 1.00 2801 138 0.2548 0.2972 REMARK 3 5 2.5900 - 2.4000 1.00 2797 140 0.2716 0.3496 REMARK 3 6 2.4000 - 2.2600 0.99 2761 148 0.2996 0.3099 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.337 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.59 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 : 0.002 2481 REMARK 3 ANGLE : 0.567 3377 REMARK 3 CHIRALITY : 0.040 374 REMARK 3 PLANARITY : 0.004 418 REMARK 3 DIHEDRAL : 15.466 346 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 8C7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292127963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976254 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17992 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 57.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.03 REMARK 200 R MERGE (I) : 0.43680 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 20.62 REMARK 200 R MERGE FOR SHELL (I) : 2.10560 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.540 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.20.1_4487 REMARK 200 STARTING MODEL: 3MTF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULFATE, 0.1M TRIS PH REMARK 280 8.5, 4% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 97.28400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.64200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.64200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 97.28400 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: MONOMERIC 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 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 SER A 199 REMARK 465 MET A 200 REMARK 465 GLN A 201 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 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 ARG A 218 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 ARG A 240 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 243 CD CE NZ REMARK 470 ARG A 273 CG CD NE CZ NH1 NH2 REMARK 470 SER A 276 OG REMARK 470 GLN A 327 CG CD OE1 NE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 GLN A 363 CG CD OE1 NE2 REMARK 470 PRO A 374 CG CD REMARK 470 VAL A 376 CG1 CG2 REMARK 470 LYS A 379 CG CD CE NZ REMARK 470 ASP A 394 CG OD1 OD2 REMARK 470 GLU A 442 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 ASP A 336 44.34 -144.99 REMARK 500 ASP A 354 93.94 69.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 8C7W A 201 499 UNP Q04771 ACVR1_HUMAN 201 499 SEQADV 8C7W SER A 199 UNP Q04771 EXPRESSION TAG SEQADV 8C7W MET A 200 UNP Q04771 EXPRESSION TAG SEQADV 8C7W ASP A 207 UNP Q04771 GLN 207 ENGINEERED MUTATION SEQRES 1 A 301 SER MET GLN ARG THR VAL ALA ARG ASP ILE THR LEU LEU SEQRES 2 A 301 GLU CYS VAL GLY LYS GLY ARG TYR GLY GLU VAL TRP ARG SEQRES 3 A 301 GLY SER TRP GLN GLY GLU ASN VAL ALA VAL LYS ILE PHE SEQRES 4 A 301 SER SER ARG ASP GLU LYS SER TRP PHE ARG GLU THR GLU SEQRES 5 A 301 LEU TYR ASN THR VAL MET LEU ARG HIS GLU ASN ILE LEU SEQRES 6 A 301 GLY PHE ILE ALA SER ASP MET THR SER ARG HIS SER SER SEQRES 7 A 301 THR GLN LEU TRP LEU ILE THR HIS TYR HIS GLU MET GLY SEQRES 8 A 301 SER LEU TYR ASP TYR LEU GLN LEU THR THR LEU ASP THR SEQRES 9 A 301 VAL SER CYS LEU ARG ILE VAL LEU SER ILE ALA SER GLY SEQRES 10 A 301 LEU ALA HIS LEU HIS ILE GLU ILE PHE GLY THR GLN GLY SEQRES 11 A 301 LYS PRO ALA ILE ALA HIS ARG ASP LEU LYS SER LYS ASN SEQRES 12 A 301 ILE LEU VAL LYS LYS ASN GLY GLN CYS CYS ILE ALA ASP SEQRES 13 A 301 LEU GLY LEU ALA VAL MET HIS SER GLN SER THR ASN GLN SEQRES 14 A 301 LEU ASP VAL GLY ASN ASN PRO ARG VAL GLY THR LYS ARG SEQRES 15 A 301 TYR MET ALA PRO GLU VAL LEU ASP GLU THR ILE GLN VAL SEQRES 16 A 301 ASP CYS PHE ASP SER TYR LYS ARG VAL ASP ILE TRP ALA SEQRES 17 A 301 PHE GLY LEU VAL LEU TRP GLU VAL ALA ARG ARG MET VAL SEQRES 18 A 301 SER ASN GLY ILE VAL GLU ASP TYR LYS PRO PRO PHE TYR SEQRES 19 A 301 ASP VAL VAL PRO ASN ASP PRO SER PHE GLU ASP MET ARG SEQRES 20 A 301 LYS VAL VAL CYS VAL ASP GLN GLN ARG PRO ASN ILE PRO SEQRES 21 A 301 ASN ARG TRP PHE SER ASP PRO THR LEU THR SER LEU ALA SEQRES 22 A 301 LYS LEU MET LYS GLU CYS TRP TYR GLN ASN PRO SER ALA SEQRES 23 A 301 ARG LEU THR ALA LEU ARG ILE LYS LYS THR LEU THR LYS SEQRES 24 A 301 ILE ASP HET U0C A 501 34 HET SO4 A 502 5 HET SO4 A 503 5 HET SO4 A 504 5 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HET EDO A 512 4 HETNAM U0C 6-METHYL-9-PIPERAZIN-1-YL-4-(3,4,5-TRIMETHOXYPHENYL)-5, HETNAM 2 U0C 7-DIHYDROPYRIDO[4,3-D][2]BENZAZEPINE HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 U0C C27 H32 N4 O3 FORMUL 3 SO4 7(O4 S 2-) FORMUL 10 EDO 4(C2 H6 O2) FORMUL 14 HOH *178(H2 O) HELIX 1 AA1 VAL A 204 ILE A 208 5 5 HELIX 2 AA2 ASP A 241 THR A 254 1 14 HELIX 3 AA3 SER A 290 THR A 298 1 9 HELIX 4 AA4 ASP A 301 ILE A 321 1 21 HELIX 5 AA5 LYS A 338 LYS A 340 5 3 HELIX 6 AA6 THR A 378 MET A 382 5 5 HELIX 7 AA7 ALA A 383 ASP A 388 1 6 HELIX 8 AA8 CYS A 395 ARG A 416 1 22 HELIX 9 AA9 SER A 440 CYS A 449 1 10 HELIX 10 AB1 PRO A 458 SER A 463 5 6 HELIX 11 AB2 ASP A 464 GLU A 476 1 13 HELIX 12 AB3 ASN A 481 ARG A 485 5 5 HELIX 13 AB4 THR A 487 ILE A 498 1 12 SHEET 1 AA1 5 THR A 209 GLY A 217 0 SHEET 2 AA1 5 GLY A 220 TRP A 227 -1 O ARG A 224 N GLU A 212 SHEET 3 AA1 5 GLU A 230 PHE A 237 -1 O VAL A 232 N GLY A 225 SHEET 4 AA1 5 SER A 276 HIS A 284 -1 O LEU A 281 N LYS A 235 SHEET 5 AA1 5 PHE A 265 ARG A 273 -1 N THR A 271 O GLN A 278 SHEET 1 AA2 3 ALA A 331 ALA A 333 0 SHEET 2 AA2 3 VAL A 359 SER A 362 -1 O HIS A 361 N ALA A 331 SHEET 3 AA2 3 GLN A 367 ASP A 369 -1 O ASP A 369 N MET A 360 SHEET 1 AA3 2 ILE A 342 VAL A 344 0 SHEET 2 AA3 2 CYS A 350 ILE A 352 -1 O CYS A 351 N LEU A 343 CRYST1 66.054 66.054 145.926 90.00 90.00 120.00 P 32 2 1 6 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 0.015139 0.008741 0.000000 0.00000 SCALE2 0.000000 0.017481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006853 0.00000