HEADER HYDROLASE 24-AUG-22 8GOD TITLE CO-CRYSTAL STRUCTURE OF HUMAN PROTEIN-ARGININE DEIMINASE TYPE-4 (PAD4) TITLE 2 WITH SMALL MOLECULE INHIBITOR JBI-589 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-ARGININE DEIMINASE TYPE-4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HL-60 PAD,PEPTIDYLARGININE DEIMINASE IV,PROTEIN-ARGININE COMPND 5 DEIMINASE TYPE IV; COMPND 6 EC: 3.5.3.15; COMPND 7 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: PADI4, PAD4, PADI5, PDI5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL MOLECULE INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SWAMINATHAN,S.BIRUDUKOTA,K.VAITHILINGAM,S.KANDAN,K.ASAITHAMBI, AUTHOR 2 N.KATHIRESAN,R.GOSU,S.RAJAGOPAL,N.SADHU REVDAT 2 29-NOV-23 8GOD 1 REMARK REVDAT 1 29-MAR-23 8GOD 0 JRNL AUTH C.GAJENDRAN,S.FUKUI,N.M.SADHU,M.ZAINUDDIN,S.RAJAGOPAL, JRNL AUTH 2 R.GOSU,S.GUTCH,S.FUKUI,C.E.SHEEHY,L.CHU,S.VISHWAKARMA, JRNL AUTH 3 D.A.JEYARAJ,G.HALLUR,D.D.WAGNER,D.SIVANANDHAN JRNL TITL ALLEVIATION OF ARTHRITIS THROUGH PREVENTION OF NEUTROPHIL JRNL TITL 2 EXTRACELLULAR TRAPS BY AN ORALLY AVAILABLE INHIBITOR OF JRNL TITL 3 PROTEIN ARGININE DEIMINASE 4. JRNL REF SCI REP V. 13 3189 2023 JRNL REFN ESSN 2045-2322 JRNL PMID 36823444 JRNL DOI 10.1038/S41598-023-30246-2 REMARK 2 REMARK 2 RESOLUTION. 2.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 18829 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.992 REMARK 3 FREE R VALUE TEST SET COUNT : 940 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1313 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.3860 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.4350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4429 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.36300 REMARK 3 B22 (A**2) : 14.04900 REMARK 3 B33 (A**2) : -9.72700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.68700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.400 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.372 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4575 ; 0.006 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4204 ; 0.002 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6249 ; 1.462 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9673 ; 1.164 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 579 ; 7.514 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;32.287 ;23.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 684 ;15.441 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.304 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 616 ; 0.052 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5212 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1000 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 879 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 53 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2163 ; 0.165 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 111 ; 0.161 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2343 ; 2.777 ; 6.603 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2342 ; 2.775 ; 6.602 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2913 ; 4.597 ; 9.884 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2914 ; 4.597 ; 9.886 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2232 ; 2.549 ; 6.681 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2233 ; 2.549 ; 6.680 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3336 ; 4.245 ; 9.954 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3337 ; 4.245 ; 9.953 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 663 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8719 -0.1207 12.2461 REMARK 3 T TENSOR REMARK 3 T11: 0.3629 T22: 0.0977 REMARK 3 T33: 0.3384 T12: 0.0048 REMARK 3 T13: -0.0468 T23: 0.0299 REMARK 3 L TENSOR REMARK 3 L11: 2.9052 L22: 0.4133 REMARK 3 L33: 3.7051 L12: -0.2257 REMARK 3 L13: -2.0226 L23: 0.2350 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: -0.5080 S13: 0.1306 REMARK 3 S21: 0.0632 S22: 0.0174 S23: -0.1077 REMARK 3 S31: -0.1236 S32: 0.3469 S33: -0.0046 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8GOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.1.018 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18844 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.880 REMARK 200 RESOLUTION RANGE LOW (A) : 46.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.04 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54000 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: MOLREP 11.7.03 REMARK 200 STARTING MODEL: 4X8G REMARK 200 REMARK 200 REMARK: THIN PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.0, 5% (V/V) TASCIMATE REMARK 280 PH 7.0, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 299K 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 39.72547 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.43950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.50066 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.72547 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.43950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 61.50066 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 MET A -27 REMARK 465 GLY A -26 REMARK 465 SER A -25 REMARK 465 SER A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 GLY A -15 REMARK 465 LEU A -14 REMARK 465 VAL A -13 REMARK 465 PRO A -12 REMARK 465 ARG A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 HIS A -8 REMARK 465 MET A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 55 REMARK 465 PRO A 56 REMARK 465 PRO A 57 REMARK 465 ALA A 58 REMARK 465 LYS A 59 REMARK 465 LYS A 60 REMARK 465 LYS A 61 REMARK 465 SER A 62 REMARK 465 THR A 63 REMARK 465 GLY A 64 REMARK 465 PRO A 129 REMARK 465 THR A 130 REMARK 465 ARG A 131 REMARK 465 ALA A 132 REMARK 465 VAL A 133 REMARK 465 LYS A 134 REMARK 465 ARG A 156 REMARK 465 ASP A 157 REMARK 465 ASN A 158 REMARK 465 LEU A 159 REMARK 465 GLU A 160 REMARK 465 SER A 161 REMARK 465 SER A 162 REMARK 465 ALA A 163 REMARK 465 MET A 164 REMARK 465 ASP A 165 REMARK 465 CYS A 166 REMARK 465 GLU A 167 REMARK 465 ASP A 168 REMARK 465 ASP A 169 REMARK 465 GLU A 170 REMARK 465 VAL A 171 REMARK 465 LEU A 172 REMARK 465 GLY A 219 REMARK 465 LYS A 220 REMARK 465 LEU A 221 REMARK 465 SER A 222 REMARK 465 SER A 223 REMARK 465 ILE A 313 REMARK 465 PHE A 314 REMARK 465 PRO A 338 REMARK 465 GLU A 339 REMARK 465 GLU A 340 REMARK 465 GLU A 341 REMARK 465 ASN A 342 REMARK 465 MET A 343 REMARK 465 ASP A 344 REMARK 465 ASP A 345 REMARK 465 GLN A 346 REMARK 465 TRP A 347 REMARK 465 ARG A 372 REMARK 465 ASN A 373 REMARK 465 ARG A 374 REMARK 465 GLY A 375 REMARK 465 LEU A 376 REMARK 465 LYS A 377 REMARK 465 GLU A 378 REMARK 465 PHE A 379 REMARK 465 PRO A 380 REMARK 465 ILE A 381 REMARK 465 LYS A 382 REMARK 465 ARG A 383 REMARK 465 VAL A 384 REMARK 465 THR A 393 REMARK 465 ARG A 394 REMARK 465 GLY A 395 REMARK 465 PRO A 396 REMARK 465 GLN A 397 REMARK 465 THR A 398 REMARK 465 GLY A 399 REMARK 465 GLY A 400 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 GLU A 12 CG CD OE1 OE2 REMARK 470 LEU A 24 CG CD1 CD2 REMARK 470 GLN A 26 CG CD OE1 NE2 REMARK 470 SER A 65 OG REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 VAL A 82 CG1 CG2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS A 126 CG CD CE NZ REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 146 CG CD OE1 NE2 REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 GLU A 175 CG CD OE1 OE2 REMARK 470 ASP A 176 CG OD1 OD2 REMARK 470 SER A 186 OG REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 ARG A 218 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ASN A 276 CG OD1 ND2 REMARK 470 ASN A 316 CG OD1 ND2 REMARK 470 PHE A 319 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 MET A 328 CG SD CE REMARK 470 LYS A 329 CG CD CE NZ REMARK 470 LYS A 331 CG CD CE NZ REMARK 470 CYS A 337 SG REMARK 470 GLN A 349 CG CD OE1 NE2 REMARK 470 GLU A 351 CG CD OE1 OE2 REMARK 470 LYS A 362 CG CD CE NZ REMARK 470 MET A 385 CG SD CE REMARK 470 ASP A 388 CG OD1 OD2 REMARK 470 PHE A 389 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 391 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 419 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 503 CG CD OE1 OE2 REMARK 470 LEU A 514 CG CD1 CD2 REMARK 470 LYS A 519 CG CD CE NZ REMARK 470 LYS A 520 CG CD CE NZ REMARK 470 LYS A 521 CG CD CE NZ REMARK 470 LYS A 522 CG CD CE NZ REMARK 470 LYS A 527 CG CD CE NZ REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 LYS A 572 CG CD CE NZ REMARK 470 ARG A 609 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 626 CG CD OE1 NE2 REMARK 470 TYR A 636 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 642 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 GLU A 12 -75.41 -60.08 REMARK 500 SER A 66 169.50 154.27 REMARK 500 ASP A 71 112.67 -29.49 REMARK 500 LYS A 81 -70.84 -82.21 REMARK 500 THR A 87 107.01 -51.46 REMARK 500 LYS A 100 42.90 -160.31 REMARK 500 PRO A 102 151.07 -41.58 REMARK 500 ASP A 120 57.96 -93.11 REMARK 500 ARG A 123 61.84 69.68 REMARK 500 GLN A 136 -168.94 -163.97 REMARK 500 ARG A 137 59.83 -99.24 REMARK 500 ASN A 153 102.96 -55.92 REMARK 500 CYS A 154 52.21 -101.85 REMARK 500 SER A 174 40.41 36.67 REMARK 500 GLU A 175 -41.53 175.78 REMARK 500 THR A 217 68.16 -154.70 REMARK 500 LYS A 232 -13.37 74.95 REMARK 500 PHE A 261 95.32 -166.20 REMARK 500 ASN A 276 109.92 -57.07 REMARK 500 ASN A 316 166.67 168.17 REMARK 500 GLU A 317 -135.45 -142.48 REMARK 500 GLU A 351 44.42 -106.45 REMARK 500 MET A 352 161.51 174.58 REMARK 500 PRO A 387 -114.92 -100.59 REMARK 500 ASP A 388 -121.78 -75.11 REMARK 500 PHE A 389 106.20 -168.52 REMARK 500 ASN A 409 43.23 -95.69 REMARK 500 SER A 437 -164.57 -105.10 REMARK 500 GLN A 455 -42.69 69.70 REMARK 500 ALA A 458 86.71 -1.57 REMARK 500 PRO A 459 152.67 -48.82 REMARK 500 ARG A 484 -125.54 49.51 REMARK 500 GLU A 503 -39.43 -36.66 REMARK 500 PHE A 515 24.72 84.80 REMARK 500 SER A 562 20.89 -72.74 REMARK 500 LYS A 574 -143.57 -80.00 REMARK 500 PRO A 584 121.29 -28.46 REMARK 500 CYS A 610 102.41 -50.19 REMARK 500 ASP A 632 64.78 31.12 REMARK 500 ILE A 638 -77.24 -90.61 REMARK 500 HIS A 640 19.50 53.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GOD A 1 663 UNP Q9UM07 PADI4_HUMAN 1 663 SEQADV 8GOD MET A -27 UNP Q9UM07 INITIATING METHIONINE SEQADV 8GOD GLY A -26 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD SER A -25 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD SER A -24 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD HIS A -23 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD HIS A -22 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD HIS A -21 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD HIS A -20 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD HIS A -19 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD HIS A -18 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD SER A -17 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD SER A -16 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD GLY A -15 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD LEU A -14 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD VAL A -13 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD PRO A -12 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD ARG A -11 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD GLY A -10 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD SER A -9 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD HIS A -8 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD MET A -7 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD GLU A -6 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD ASN A -5 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD LEU A -4 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD TYR A -3 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD PHE A -2 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD GLN A -1 UNP Q9UM07 EXPRESSION TAG SEQADV 8GOD GLY A 0 UNP Q9UM07 EXPRESSION TAG SEQRES 1 A 691 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 691 LEU VAL PRO ARG GLY SER HIS MET GLU ASN LEU TYR PHE SEQRES 3 A 691 GLN GLY MET ALA GLN GLY THR LEU ILE ARG VAL THR PRO SEQRES 4 A 691 GLU GLN PRO THR HIS ALA VAL CYS VAL LEU GLY THR LEU SEQRES 5 A 691 THR GLN LEU ASP ILE CYS SER SER ALA PRO GLU ASP CYS SEQRES 6 A 691 THR SER PHE SER ILE ASN ALA SER PRO GLY VAL VAL VAL SEQRES 7 A 691 ASP ILE ALA HIS GLY PRO PRO ALA LYS LYS LYS SER THR SEQRES 8 A 691 GLY SER SER THR TRP PRO LEU ASP PRO GLY VAL GLU VAL SEQRES 9 A 691 THR LEU THR MET LYS VAL ALA SER GLY SER THR GLY ASP SEQRES 10 A 691 GLN LYS VAL GLN ILE SER TYR TYR GLY PRO LYS THR PRO SEQRES 11 A 691 PRO VAL LYS ALA LEU LEU TYR LEU THR GLY VAL GLU ILE SEQRES 12 A 691 SER LEU CYS ALA ASP ILE THR ARG THR GLY LYS VAL LYS SEQRES 13 A 691 PRO THR ARG ALA VAL LYS ASP GLN ARG THR TRP THR TRP SEQRES 14 A 691 GLY PRO CYS GLY GLN GLY ALA ILE LEU LEU VAL ASN CYS SEQRES 15 A 691 ASP ARG ASP ASN LEU GLU SER SER ALA MET ASP CYS GLU SEQRES 16 A 691 ASP ASP GLU VAL LEU ASP SER GLU ASP LEU GLN ASP MET SEQRES 17 A 691 SER LEU MET THR LEU SER THR LYS THR PRO LYS ASP PHE SEQRES 18 A 691 PHE THR ASN HIS THR LEU VAL LEU HIS VAL ALA ARG SER SEQRES 19 A 691 GLU MET ASP LYS VAL ARG VAL PHE GLN ALA THR ARG GLY SEQRES 20 A 691 LYS LEU SER SER LYS CYS SER VAL VAL LEU GLY PRO LYS SEQRES 21 A 691 TRP PRO SER HIS TYR LEU MET VAL PRO GLY GLY LYS HIS SEQRES 22 A 691 ASN MET ASP PHE TYR VAL GLU ALA LEU ALA PHE PRO ASP SEQRES 23 A 691 THR ASP PHE PRO GLY LEU ILE THR LEU THR ILE SER LEU SEQRES 24 A 691 LEU ASP THR SER ASN LEU GLU LEU PRO GLU ALA VAL VAL SEQRES 25 A 691 PHE GLN ASP SER VAL VAL PHE ARG VAL ALA PRO TRP ILE SEQRES 26 A 691 MET THR PRO ASN THR GLN PRO PRO GLN GLU VAL TYR ALA SEQRES 27 A 691 CYS SER ILE PHE GLU ASN GLU ASP PHE LEU LYS SER VAL SEQRES 28 A 691 THR THR LEU ALA MET LYS ALA LYS CYS LYS LEU THR ILE SEQRES 29 A 691 CYS PRO GLU GLU GLU ASN MET ASP ASP GLN TRP MET GLN SEQRES 30 A 691 ASP GLU MET GLU ILE GLY TYR ILE GLN ALA PRO HIS LYS SEQRES 31 A 691 THR LEU PRO VAL VAL PHE ASP SER PRO ARG ASN ARG GLY SEQRES 32 A 691 LEU LYS GLU PHE PRO ILE LYS ARG VAL MET GLY PRO ASP SEQRES 33 A 691 PHE GLY TYR VAL THR ARG GLY PRO GLN THR GLY GLY ILE SEQRES 34 A 691 SER GLY LEU ASP SER PHE GLY ASN LEU GLU VAL SER PRO SEQRES 35 A 691 PRO VAL THR VAL ARG GLY LYS GLU TYR PRO LEU GLY ARG SEQRES 36 A 691 ILE LEU PHE GLY ASP SER CYS TYR PRO SER ASN ASP SER SEQRES 37 A 691 ARG GLN MET HIS GLN ALA LEU GLN ASP PHE LEU SER ALA SEQRES 38 A 691 GLN GLN VAL GLN ALA PRO VAL LYS LEU TYR SER ASP TRP SEQRES 39 A 691 LEU SER VAL GLY HIS VAL ASP GLU PHE LEU SER PHE VAL SEQRES 40 A 691 PRO ALA PRO ASP ARG LYS GLY PHE ARG LEU LEU LEU ALA SEQRES 41 A 691 SER PRO ARG SER CYS TYR LYS LEU PHE GLN GLU GLN GLN SEQRES 42 A 691 ASN GLU GLY HIS GLY GLU ALA LEU LEU PHE GLU GLY ILE SEQRES 43 A 691 LYS LYS LYS LYS GLN GLN LYS ILE LYS ASN ILE LEU SER SEQRES 44 A 691 ASN LYS THR LEU ARG GLU HIS ASN SER PHE VAL GLU ARG SEQRES 45 A 691 CYS ILE ASP TRP ASN ARG GLU LEU LEU LYS ARG GLU LEU SEQRES 46 A 691 GLY LEU ALA GLU SER ASP ILE ILE ASP ILE PRO GLN LEU SEQRES 47 A 691 PHE LYS LEU LYS GLU PHE SER LYS ALA GLU ALA PHE PHE SEQRES 48 A 691 PRO ASN MET VAL ASN MET LEU VAL LEU GLY LYS HIS LEU SEQRES 49 A 691 GLY ILE PRO LYS PRO PHE GLY PRO VAL ILE ASN GLY ARG SEQRES 50 A 691 CYS CYS LEU GLU GLU LYS VAL CYS SER LEU LEU GLU PRO SEQRES 51 A 691 LEU GLY LEU GLN CYS THR PHE ILE ASN ASP PHE PHE THR SEQRES 52 A 691 TYR HIS ILE ARG HIS GLY GLU VAL HIS CYS GLY THR ASN SEQRES 53 A 691 VAL ARG ARG LYS PRO PHE SER PHE LYS TRP TRP ASN MET SEQRES 54 A 691 VAL PRO HET K3X A 701 36 HETNAM K3X [(3~{R})-3-AZANYLPIPERIDIN-1-YL]-[2-[1-[(4- HETNAM 2 K3X FLUOROPHENYL)METHYL]INDOL-2-YL]-3-METHYL-IMIDAZO[1,2- HETNAM 3 K3X A]PYRIDIN-7-YL]METHANONE FORMUL 2 K3X C29 H28 F N5 O FORMUL 3 HOH *4(H2 O) HELIX 1 AA1 ASP A 192 THR A 195 5 4 HELIX 2 AA2 GLU A 207 ASP A 209 5 3 HELIX 3 AA3 ASP A 318 ALA A 330 1 13 HELIX 4 AA4 MET A 348 MET A 352 5 5 HELIX 5 AA5 SER A 406 LEU A 410 5 5 HELIX 6 AA6 HIS A 444 GLN A 454 1 11 HELIX 7 AA7 HIS A 471 GLU A 474 5 4 HELIX 8 AA8 PRO A 494 ASN A 506 1 13 HELIX 9 AA9 GLU A 507 GLU A 511 5 5 HELIX 10 AB1 ILE A 526 SER A 531 1 6 HELIX 11 AB2 ASN A 532 LEU A 557 1 26 HELIX 12 AB3 ALA A 560 SER A 562 5 3 HELIX 13 AB4 GLU A 575 SER A 577 5 3 HELIX 14 AB5 CYS A 610 GLU A 621 1 12 HELIX 15 AB6 PRO A 622 GLY A 624 5 3 HELIX 16 AB7 LYS A 657 MET A 661 5 5 SHEET 1 AA1 4 LEU A 6 ARG A 8 0 SHEET 2 AA1 4 THR A 25 ASP A 28 1 O ASP A 28 N ILE A 7 SHEET 3 AA1 4 GLU A 75 MET A 80 -1 O LEU A 78 N THR A 25 SHEET 4 AA1 4 VAL A 48 ALA A 53 -1 N VAL A 49 O THR A 79 SHEET 1 AA2 5 THR A 15 VAL A 20 0 SHEET 2 AA2 5 VAL A 104 CYS A 118 1 O TYR A 109 N THR A 15 SHEET 3 AA2 5 GLN A 90 TYR A 97 -1 N VAL A 92 O LEU A 108 SHEET 4 AA2 5 SER A 39 ALA A 44 -1 N ASN A 43 O GLN A 93 SHEET 5 AA2 5 TRP A 68 PRO A 69 -1 O TRP A 68 N PHE A 40 SHEET 1 AA3 6 THR A 15 VAL A 20 0 SHEET 2 AA3 6 VAL A 104 CYS A 118 1 O TYR A 109 N THR A 15 SHEET 3 AA3 6 SER A 181 LYS A 188 -1 O THR A 184 N CYS A 118 SHEET 4 AA3 6 HIS A 245 ALA A 253 -1 O PHE A 249 N MET A 183 SHEET 5 AA3 6 VAL A 211 GLN A 215 -1 N PHE A 214 O TYR A 250 SHEET 6 AA3 6 VAL A 227 LEU A 229 -1 O LEU A 229 N VAL A 213 SHEET 1 AA4 5 ALA A 148 LEU A 150 0 SHEET 2 AA4 5 ALA A 282 VAL A 293 1 O ARG A 292 N ALA A 148 SHEET 3 AA4 5 LEU A 264 ASP A 273 -1 N ILE A 269 O ASP A 287 SHEET 4 AA4 5 HIS A 197 VAL A 203 -1 N HIS A 202 O THR A 268 SHEET 5 AA4 5 SER A 235 TYR A 237 -1 O HIS A 236 N LEU A 201 SHEET 1 AA5 3 LYS A 333 THR A 335 0 SHEET 2 AA5 3 PRO A 305 TYR A 309 1 N VAL A 308 O LYS A 333 SHEET 3 AA5 3 ASN A 648 ARG A 651 -1 O ARG A 650 N GLN A 306 SHEET 1 AA6 3 GLU A 353 ALA A 359 0 SHEET 2 AA6 3 LYS A 362 PHE A 368 -1 O LYS A 362 N ALA A 359 SHEET 3 AA6 3 TYR A 391 VAL A 392 1 O VAL A 392 N VAL A 367 SHEET 1 AA7 3 GLU A 411 VAL A 412 0 SHEET 2 AA7 3 ILE A 428 ASP A 432 -1 O LEU A 429 N GLU A 411 SHEET 3 AA7 3 VAL A 460 TYR A 463 1 O LEU A 462 N PHE A 430 SHEET 1 AA8 2 VAL A 416 VAL A 418 0 SHEET 2 AA8 2 LYS A 421 TYR A 423 -1 O LYS A 421 N VAL A 418 SHEET 1 AA9 3 LEU A 476 PRO A 480 0 SHEET 2 AA9 3 PHE A 487 SER A 493 -1 O LEU A 490 N SER A 477 SHEET 3 AA9 3 ILE A 564 PRO A 568 1 O ILE A 565 N LEU A 489 SHEET 1 AB1 2 LEU A 513 LEU A 514 0 SHEET 2 AB1 2 GLN A 524 LYS A 525 -1 O GLN A 524 N LEU A 514 SHEET 1 AB2 2 PHE A 571 LEU A 573 0 SHEET 2 AB2 2 ALA A 579 ALA A 581 -1 O GLU A 580 N LYS A 572 SHEET 1 AB3 3 LEU A 590 LEU A 592 0 SHEET 2 AB3 3 HIS A 595 PRO A 599 -1 O GLY A 597 N LEU A 590 SHEET 3 AB3 3 GLN A 626 ILE A 630 1 O THR A 628 N LEU A 596 SHEET 1 AB4 2 PHE A 634 THR A 635 0 SHEET 2 AB4 2 HIS A 644 CYS A 645 -1 O HIS A 644 N THR A 635 CRYST1 111.456 60.879 127.097 90.00 104.59 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 0.008972 0.000000 0.002335 0.00000 SCALE2 0.000000 0.016426 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008130 0.00000