HEADER HYDROLASE/HYDROLASE INHIBITOR 10-DEC-14 4X8C TITLE CRYSTAL STRUCTURE OF HUMAN PEPTIDYLARGININE DEIMINASE TYPE4 (PAD4) IN TITLE 2 COMPLEX WITH GSK147 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; COMPND 8 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: PADI4, PADI5, PDI5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.D.LEWIS,B.D.BAX,C.-W.CHUNG,O.POLYAKOVA,J.THORPE REVDAT 5 18-APR-18 4X8C 1 REMARK REVDAT 4 22-NOV-17 4X8C 1 SOURCE REMARK REVDAT 3 25-FEB-15 4X8C 1 JRNL REVDAT 2 11-FEB-15 4X8C 1 JRNL REVDAT 1 28-JAN-15 4X8C 0 JRNL AUTH H.D.LEWIS,J.LIDDLE,J.E.COOTE,S.J.ATKINSON,M.D.BARKER, JRNL AUTH 2 B.D.BAX,K.L.BICKER,R.P.BINGHAM,M.CAMPBELL,Y.H.CHEN, JRNL AUTH 3 C.W.CHUNG,P.D.CRAGGS,R.P.DAVIS,D.EBERHARD,G.JOBERTY, JRNL AUTH 4 K.E.LIND,K.LOCKE,C.MALLER,K.MARTINOD,C.PATTEN,O.POLYAKOVA, JRNL AUTH 5 C.E.RISE,M.RUDIGER,R.J.SHEPPARD,D.J.SLADE,P.THOMAS,J.THORPE, JRNL AUTH 6 G.YAO,G.DREWES,D.D.WAGNER,P.R.THOMPSON,R.K.PRINJHA, JRNL AUTH 7 D.M.WILSON JRNL TITL INHIBITION OF PAD4 ACTIVITY IS SUFFICIENT TO DISRUPT MOUSE JRNL TITL 2 AND HUMAN NET FORMATION. JRNL REF NAT.CHEM.BIOL. V. 11 189 2015 JRNL REFN ESSN 1552-4469 JRNL PMID 25622091 JRNL DOI 10.1038/NCHEMBIO.1735 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 14417 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 710 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 19.8361 - 5.2743 0.91 2668 166 0.1894 0.2334 REMARK 3 2 5.2743 - 4.1994 0.95 2777 120 0.1711 0.2318 REMARK 3 3 4.1994 - 3.6724 0.95 2729 140 0.1851 0.2281 REMARK 3 4 3.6724 - 3.3383 0.97 2744 149 0.2421 0.2748 REMARK 3 5 3.3383 - 3.1000 0.97 2789 135 0.2854 0.3609 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.780 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) : 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 4265 REMARK 3 ANGLE : 0.519 5827 REMARK 3 CHIRALITY : 0.020 685 REMARK 3 PLANARITY : 0.003 744 REMARK 3 DIHEDRAL : 10.889 1445 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 3:112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0510 18.0950 -41.0369 REMARK 3 T TENSOR REMARK 3 T11: 1.5702 T22: 2.1701 REMARK 3 T33: 0.8765 T12: -0.0787 REMARK 3 T13: -0.0439 T23: -0.2147 REMARK 3 L TENSOR REMARK 3 L11: 2.6660 L22: 2.2811 REMARK 3 L33: 6.2608 L12: 1.4958 REMARK 3 L13: 1.9009 L23: 1.5004 REMARK 3 S TENSOR REMARK 3 S11: -0.2662 S12: 1.0638 S13: -0.6989 REMARK 3 S21: -0.4247 S22: -0.0025 S23: 0.0845 REMARK 3 S31: 1.1507 S32: -2.1610 S33: -0.2289 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 113:292 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6770 35.2370 -22.6500 REMARK 3 T TENSOR REMARK 3 T11: 0.9016 T22: 0.7489 REMARK 3 T33: 0.7878 T12: -0.0233 REMARK 3 T13: 0.0592 T23: 0.2142 REMARK 3 L TENSOR REMARK 3 L11: 4.6191 L22: 0.6948 REMARK 3 L33: 8.3827 L12: 0.2652 REMARK 3 L13: 1.6513 L23: 1.1759 REMARK 3 S TENSOR REMARK 3 S11: 0.0382 S12: 1.5368 S13: 0.2627 REMARK 3 S21: -0.5236 S22: 0.0970 S23: -0.1575 REMARK 3 S31: -0.0712 S32: 0.9491 S33: 0.1036 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 308:336 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.0500 37.9663 11.5215 REMARK 3 T TENSOR REMARK 3 T11: 0.5737 T22: 2.4898 REMARK 3 T33: 1.4465 T12: -0.2693 REMARK 3 T13: 0.1063 T23: -0.0614 REMARK 3 L TENSOR REMARK 3 L11: 3.4874 L22: 4.9829 REMARK 3 L33: 3.8638 L12: -0.7045 REMARK 3 L13: 3.3254 L23: -2.4997 REMARK 3 S TENSOR REMARK 3 S11: 0.2128 S12: -0.0275 S13: -0.3401 REMARK 3 S21: -0.2238 S22: -0.2201 S23: -0.1346 REMARK 3 S31: 0.2725 S32: 1.8948 S33: 0.0526 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 351:390 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6471 37.2291 -1.2423 REMARK 3 T TENSOR REMARK 3 T11: 0.7882 T22: 0.9960 REMARK 3 T33: 0.9250 T12: -0.2622 REMARK 3 T13: 0.0062 T23: -0.0715 REMARK 3 L TENSOR REMARK 3 L11: 5.0139 L22: 3.4137 REMARK 3 L33: 2.7888 L12: 0.6947 REMARK 3 L13: 1.8723 L23: 2.0937 REMARK 3 S TENSOR REMARK 3 S11: 0.4448 S12: -0.3851 S13: 0.7343 REMARK 3 S21: 0.2692 S22: -0.4048 S23: -0.3066 REMARK 3 S31: 0.2551 S32: 0.7020 S33: 0.0524 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 405:492 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8568 33.2838 15.5664 REMARK 3 T TENSOR REMARK 3 T11: 0.8164 T22: 0.7439 REMARK 3 T33: 0.7734 T12: -0.0947 REMARK 3 T13: -0.0614 T23: -0.0225 REMARK 3 L TENSOR REMARK 3 L11: 6.5050 L22: 0.9571 REMARK 3 L33: 7.0352 L12: 0.5809 REMARK 3 L13: -0.4419 L23: -1.0467 REMARK 3 S TENSOR REMARK 3 S11: -0.0204 S12: -1.3279 S13: 0.7990 REMARK 3 S21: 0.1405 S22: 0.0827 S23: 0.1447 REMARK 3 S31: -0.5364 S32: 0.3625 S33: 0.0389 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 495:645 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.0145 34.3431 30.4938 REMARK 3 T TENSOR REMARK 3 T11: 1.1793 T22: 2.1794 REMARK 3 T33: 1.1817 T12: -0.0781 REMARK 3 T13: -0.1411 T23: -0.1305 REMARK 3 L TENSOR REMARK 3 L11: 3.9902 L22: 1.5759 REMARK 3 L33: 4.9708 L12: 1.1208 REMARK 3 L13: 1.2799 L23: 0.5049 REMARK 3 S TENSOR REMARK 3 S11: 0.3515 S12: -1.6980 S13: 0.5561 REMARK 3 S21: 0.7498 S22: -0.1824 S23: -0.6244 REMARK 3 S31: 0.2330 S32: 2.1920 S33: 0.0215 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 4X8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000204779. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14431 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3APN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM IMIDAZOLE, PH 7.8, 200 MM REMARK 280 LI2SO4, 2 MM TCEP, 6-7.5% PEG 2K MME, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 72.75000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.75000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.21000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 GLY A -7 REMARK 465 PRO A -6 REMARK 465 LEU A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 PRO A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 34 REMARK 465 GLU A 35 REMARK 465 ASP A 36 REMARK 465 ALA A 53 REMARK 465 HIS A 54 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 SER A 65 REMARK 465 SER A 66 REMARK 465 THR A 67 REMARK 465 ASP A 71 REMARK 465 PRO A 72 REMARK 465 GLY A 73 REMARK 465 VAL A 74 REMARK 465 GLY A 98 REMARK 465 PRO A 99 REMARK 465 LYS A 100 REMARK 465 THR A 101 REMARK 465 PRO A 102 REMARK 465 THR A 130 REMARK 465 ARG A 131 REMARK 465 ALA A 132 REMARK 465 VAL A 133 REMARK 465 ASP A 155 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 SER A 312 REMARK 465 ILE A 313 REMARK 465 PHE A 314 REMARK 465 GLU A 315 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 MET A 348 REMARK 465 GLN A 349 REMARK 465 PRO A 371 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 MET A 385 REMARK 465 GLY A 386 REMARK 465 PRO A 387 REMARK 465 ASP A 388 REMARK 465 VAL A 392 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 465 ILE A 401 REMARK 465 GLY A 517 REMARK 465 ILE A 518 REMARK 465 LYS A 519 REMARK 465 LYS A 520 REMARK 465 LYS A 521 REMARK 465 GLY A 603 REMARK 465 PRO A 604 REMARK 465 VAL A 605 REMARK 465 ILE A 606 REMARK 465 ASN A 607 REMARK 465 GLY A 608 REMARK 465 ARG A 609 REMARK 465 ARG A 639 REMARK 465 HIS A 640 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 CD OE1 OE2 REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 GLN A 26 CG CD OE1 NE2 REMARK 470 TRP A 68 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 68 CZ3 CH2 REMARK 470 GLU A 75 CG CD OE1 OE2 REMARK 470 VAL A 82 CG1 CG2 REMARK 470 LYS A 91 CG CD CE NZ REMARK 470 GLN A 93 CG CD OE1 NE2 REMARK 470 TYR A 96 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 LYS A 126 CG CD CE NZ REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 GLN A 136 CG CD OE1 NE2 REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 146 CG CD OE1 NE2 REMARK 470 ASP A 173 CG OD1 OD2 REMARK 470 GLU A 175 CG CD OE1 OE2 REMARK 470 GLN A 178 CG CD OE1 NE2 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 220 CG CD CE NZ REMARK 470 LEU A 221 CG CD1 CD2 REMARK 470 SER A 223 OG REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 MET A 239 CG SD CE REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 GLU A 281 CG CD OE1 OE2 REMARK 470 CYS A 311 SG REMARK 470 ASN A 316 CG OD1 ND2 REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 ASP A 318 CG OD1 OD2 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 ASP A 350 CG OD1 OD2 REMARK 470 GLU A 351 CG CD OE1 OE2 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 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 442 CG CD OE1 NE2 REMARK 470 GLN A 502 CG CD OE1 NE2 REMARK 470 ASN A 506 CG OD1 ND2 REMARK 470 GLU A 507 CG CD OE1 OE2 REMARK 470 GLU A 511 CG CD OE1 OE2 REMARK 470 LEU A 513 CG CD1 CD2 REMARK 470 LEU A 514 CG CD1 CD2 REMARK 470 GLU A 516 CG CD OE1 OE2 REMARK 470 LYS A 522 CG CD CE NZ REMARK 470 GLN A 524 CG CD OE1 NE2 REMARK 470 LYS A 525 CG CD CE NZ REMARK 470 LYS A 527 CG CD CE NZ REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 GLU A 537 CG CD OE1 OE2 REMARK 470 LYS A 574 CG CD CE NZ REMARK 470 LYS A 600 CG CD CE NZ REMARK 470 GLU A 614 CG CD OE1 OE2 REMARK 470 GLN A 626 CG CD OE1 NE2 REMARK 470 LYS A 652 CG CD CE NZ 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 ILE A 29 -50.07 -123.19 REMARK 500 THR A 38 -52.82 -127.48 REMARK 500 CYS A 144 37.86 -91.27 REMARK 500 PRO A 231 19.56 -68.81 REMARK 500 LYS A 232 -22.50 -149.35 REMARK 500 GLN A 306 -42.44 -132.08 REMARK 500 GLU A 317 -59.04 -135.52 REMARK 500 LYS A 331 70.74 56.44 REMARK 500 ALA A 458 109.93 -56.87 REMARK 500 ASP A 483 -168.56 -114.43 REMARK 500 ARG A 484 -130.07 55.14 REMARK 500 HIS A 509 40.25 -108.96 REMARK 500 ASN A 532 96.85 -63.60 REMARK 500 SER A 577 19.37 58.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 814 DISTANCE = 5.81 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 353 OE1 REMARK 620 2 PHE A 407 O 68.4 REMARK 620 3 LEU A 410 O 77.2 67.6 REMARK 620 4 GLU A 411 OE1 128.2 128.0 70.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3YZ A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X8G RELATED DB: PDB DBREF 4X8C A 1 663 UNP Q9UM07 PADI4_HUMAN 1 663 SEQADV 4X8C GLY A -7 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C PRO A -6 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C LEU A -5 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C GLY A -4 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C SER A -3 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C PRO A -2 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C GLU A -1 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C PHE A 0 UNP Q9UM07 EXPRESSION TAG SEQADV 4X8C ALA A 645 UNP Q9UM07 CYS 645 ENGINEERED MUTATION SEQRES 1 A 671 GLY PRO LEU GLY SER PRO GLU PHE MET ALA GLN GLY THR SEQRES 2 A 671 LEU ILE ARG VAL THR PRO GLU GLN PRO THR HIS ALA VAL SEQRES 3 A 671 CYS VAL LEU GLY THR LEU THR GLN LEU ASP ILE CYS SER SEQRES 4 A 671 SER ALA PRO GLU ASP CYS THR SER PHE SER ILE ASN ALA SEQRES 5 A 671 SER PRO GLY VAL VAL VAL ASP ILE ALA HIS GLY PRO PRO SEQRES 6 A 671 ALA LYS LYS LYS SER THR GLY SER SER THR TRP PRO LEU SEQRES 7 A 671 ASP PRO GLY VAL GLU VAL THR LEU THR MET LYS VAL ALA SEQRES 8 A 671 SER GLY SER THR GLY ASP GLN LYS VAL GLN ILE SER TYR SEQRES 9 A 671 TYR GLY PRO LYS THR PRO PRO VAL LYS ALA LEU LEU TYR SEQRES 10 A 671 LEU THR GLY VAL GLU ILE SER LEU CYS ALA ASP ILE THR SEQRES 11 A 671 ARG THR GLY LYS VAL LYS PRO THR ARG ALA VAL LYS ASP SEQRES 12 A 671 GLN ARG THR TRP THR TRP GLY PRO CYS GLY GLN GLY ALA SEQRES 13 A 671 ILE LEU LEU VAL ASN CYS ASP ARG ASP ASN LEU GLU SER SEQRES 14 A 671 SER ALA MET ASP CYS GLU ASP ASP GLU VAL LEU ASP SER SEQRES 15 A 671 GLU ASP LEU GLN ASP MET SER LEU MET THR LEU SER THR SEQRES 16 A 671 LYS THR PRO LYS ASP PHE PHE THR ASN HIS THR LEU VAL SEQRES 17 A 671 LEU HIS VAL ALA ARG SER GLU MET ASP LYS VAL ARG VAL SEQRES 18 A 671 PHE GLN ALA THR ARG GLY LYS LEU SER SER LYS CYS SER SEQRES 19 A 671 VAL VAL LEU GLY PRO LYS TRP PRO SER HIS TYR LEU MET SEQRES 20 A 671 VAL PRO GLY GLY LYS HIS ASN MET ASP PHE TYR VAL GLU SEQRES 21 A 671 ALA LEU ALA PHE PRO ASP THR ASP PHE PRO GLY LEU ILE SEQRES 22 A 671 THR LEU THR ILE SER LEU LEU ASP THR SER ASN LEU GLU SEQRES 23 A 671 LEU PRO GLU ALA VAL VAL PHE GLN ASP SER VAL VAL PHE SEQRES 24 A 671 ARG VAL ALA PRO TRP ILE MET THR PRO ASN THR GLN PRO SEQRES 25 A 671 PRO GLN GLU VAL TYR ALA CYS SER ILE PHE GLU ASN GLU SEQRES 26 A 671 ASP PHE LEU LYS SER VAL THR THR LEU ALA MET LYS ALA SEQRES 27 A 671 LYS CYS LYS LEU THR ILE CYS PRO GLU GLU GLU ASN MET SEQRES 28 A 671 ASP ASP GLN TRP MET GLN ASP GLU MET GLU ILE GLY TYR SEQRES 29 A 671 ILE GLN ALA PRO HIS LYS THR LEU PRO VAL VAL PHE ASP SEQRES 30 A 671 SER PRO ARG ASN ARG GLY LEU LYS GLU PHE PRO ILE LYS SEQRES 31 A 671 ARG VAL MET GLY PRO ASP PHE GLY TYR VAL THR ARG GLY SEQRES 32 A 671 PRO GLN THR GLY GLY ILE SER GLY LEU ASP SER PHE GLY SEQRES 33 A 671 ASN LEU GLU VAL SER PRO PRO VAL THR VAL ARG GLY LYS SEQRES 34 A 671 GLU TYR PRO LEU GLY ARG ILE LEU PHE GLY ASP SER CYS SEQRES 35 A 671 TYR PRO SER ASN ASP SER ARG GLN MET HIS GLN ALA LEU SEQRES 36 A 671 GLN ASP PHE LEU SER ALA GLN GLN VAL GLN ALA PRO VAL SEQRES 37 A 671 LYS LEU TYR SER ASP TRP LEU SER VAL GLY HIS VAL ASP SEQRES 38 A 671 GLU PHE LEU SER PHE VAL PRO ALA PRO ASP ARG LYS GLY SEQRES 39 A 671 PHE ARG LEU LEU LEU ALA SER PRO ARG SER CYS TYR LYS SEQRES 40 A 671 LEU PHE GLN GLU GLN GLN ASN GLU GLY HIS GLY GLU ALA SEQRES 41 A 671 LEU LEU PHE GLU GLY ILE LYS LYS LYS LYS GLN GLN LYS SEQRES 42 A 671 ILE LYS ASN ILE LEU SER ASN LYS THR LEU ARG GLU HIS SEQRES 43 A 671 ASN SER PHE VAL GLU ARG CYS ILE ASP TRP ASN ARG GLU SEQRES 44 A 671 LEU LEU LYS ARG GLU LEU GLY LEU ALA GLU SER ASP ILE SEQRES 45 A 671 ILE ASP ILE PRO GLN LEU PHE LYS LEU LYS GLU PHE SER SEQRES 46 A 671 LYS ALA GLU ALA PHE PHE PRO ASN MET VAL ASN MET LEU SEQRES 47 A 671 VAL LEU GLY LYS HIS LEU GLY ILE PRO LYS PRO PHE GLY SEQRES 48 A 671 PRO VAL ILE ASN GLY ARG CYS CYS LEU GLU GLU LYS VAL SEQRES 49 A 671 CYS SER LEU LEU GLU PRO LEU GLY LEU GLN CYS THR PHE SEQRES 50 A 671 ILE ASN ASP PHE PHE THR TYR HIS ILE ARG HIS GLY GLU SEQRES 51 A 671 VAL HIS ALA GLY THR ASN VAL ARG ARG LYS PRO PHE SER SEQRES 52 A 671 PHE LYS TRP TRP ASN MET VAL PRO HET CA A 701 1 HET CA A 702 1 HET 3YZ A 703 35 HETNAM CA CALCIUM ION HETNAM 3YZ [(3S,4R)-3-AMINO-4-HYDROXYPIPERIDIN-1-YL]{2-[1- HETNAM 2 3YZ (CYCLOPROPYLMETHYL)-1H-PYRROLO[2,3-B]PYRIDIN-2-YL]-7- HETNAM 3 3YZ METHOXY-1-METHYL-1H-BENZIMIDAZOL-5-YL}METHANONE FORMUL 2 CA 2(CA 2+) FORMUL 4 3YZ C26 H30 N6 O3 FORMUL 5 HOH *23(H2 O) HELIX 1 AA1 ILE A 29 ALA A 33 5 5 HELIX 2 AA2 SER A 174 GLN A 178 1 5 HELIX 3 AA3 ASP A 192 THR A 195 5 4 HELIX 4 AA4 GLU A 317 ALA A 330 1 14 HELIX 5 AA5 HIS A 444 GLN A 454 1 11 HELIX 6 AA6 HIS A 471 GLU A 474 5 4 HELIX 7 AA7 PRO A 494 GLY A 508 1 15 HELIX 8 AA8 LYS A 525 ASN A 532 1 8 HELIX 9 AA9 ASN A 532 LEU A 557 1 26 HELIX 10 AB1 ALA A 560 SER A 562 5 3 HELIX 11 AB2 GLU A 575 SER A 577 5 3 HELIX 12 AB3 CYS A 611 GLU A 621 1 11 HELIX 13 AB4 PRO A 622 GLY A 624 5 3 HELIX 14 AB5 LYS A 657 MET A 661 5 5 SHEET 1 AA1 4 GLY A 4 ARG A 8 0 SHEET 2 AA1 4 LEU A 24 ASP A 28 1 O ASP A 28 N ILE A 7 SHEET 3 AA1 4 VAL A 76 MET A 80 -1 O VAL A 76 N LEU A 27 SHEET 4 AA1 4 VAL A 48 ASP A 51 -1 N VAL A 49 O THR A 79 SHEET 1 AA2 4 THR A 15 VAL A 20 0 SHEET 2 AA2 4 VAL A 104 CYS A 118 1 O THR A 111 N CYS A 19 SHEET 3 AA2 4 GLN A 90 TYR A 96 -1 N ILE A 94 O ALA A 106 SHEET 4 AA2 4 PHE A 40 ALA A 44 -1 N SER A 41 O SER A 95 SHEET 1 AA3 6 THR A 15 VAL A 20 0 SHEET 2 AA3 6 VAL A 104 CYS A 118 1 O THR A 111 N CYS A 19 SHEET 3 AA3 6 SER A 181 THR A 189 -1 O THR A 184 N CYS A 118 SHEET 4 AA3 6 GLY A 243 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 VAL A 228 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 LEU A 150 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 THR A 198 O LEU A 272 SHEET 5 AA4 5 SER A 235 LEU A 238 -1 O LEU A 238 N LEU A 199 SHEET 1 AA5 3 LYS A 333 ILE A 336 0 SHEET 2 AA5 3 PRO A 305 ALA A 310 1 N VAL A 308 O LYS A 333 SHEET 3 AA5 3 THR A 647 ARG A 651 -1 O ASN A 648 N TYR A 309 SHEET 1 AA6 2 GLU A 353 GLN A 358 0 SHEET 2 AA6 2 THR A 363 PHE A 368 -1 O LEU A 364 N ILE A 357 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 567 N LEU A 491 SHEET 1 AB1 2 PHE A 571 LEU A 573 0 SHEET 2 AB1 2 ALA A 579 ALA A 581 -1 O GLU A 580 N LYS A 572 SHEET 1 AB2 3 LEU A 590 VAL A 591 0 SHEET 2 AB2 3 HIS A 595 GLY A 597 -1 O GLY A 597 N LEU A 590 SHEET 3 AB2 3 GLN A 626 CYS A 627 1 O GLN A 626 N LEU A 596 SHEET 1 AB3 2 THR A 635 HIS A 637 0 SHEET 2 AB3 2 GLU A 642 HIS A 644 -1 O GLU A 642 N HIS A 637 LINK OD1 ASP A 176 CA CA A 702 1555 1555 2.60 LINK OE1 GLU A 353 CA CA A 701 1555 1555 2.89 LINK O PHE A 407 CA CA A 701 1555 1555 2.87 LINK O LEU A 410 CA CA A 701 1555 1555 3.09 LINK OE1 GLU A 411 CA CA A 701 1555 1555 3.11 CISPEP 1 LYS A 134 ASP A 135 0 0.21 SITE 1 AC1 4 GLU A 353 PHE A 407 LEU A 410 GLU A 411 SITE 1 AC2 3 ASN A 153 ASP A 176 ASP A 179 SITE 1 AC3 11 VAL A 469 HIS A 471 ASP A 473 PHE A 515 SITE 2 AC3 11 ALA A 581 PHE A 582 PRO A 584 ASN A 585 SITE 3 AC3 11 ASN A 588 PHE A 634 VAL A 643 CRYST1 145.500 60.420 113.310 90.00 123.13 90.00 C 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 0.006873 0.000000 0.004485 0.00000 SCALE2 0.000000 0.016551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010539 0.00000 MASTER 557 0 3 14 39 0 5 6 0 0 0 52 END