HEADER HYDROLASE/HYDROLASE INHIBITOR 03-FEB-17 5N0Y TITLE HPAD4 CRYSTAL COMPLEX WITH AFM-30A 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, PAD4, PADI5, PDI5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.BEAUMONT,P.KERRY,P.THOMPSON,A.MUTH,V.SUBRAMANIAN,M.NAGAR,H.SRINATH, AUTHOR 2 K.CLANCY,S.PARELKAR REVDAT 1 24-MAY-17 5N0Y 0 JRNL AUTH A.MUTH,V.SUBRAMANIAN,E.BEAUMONT,M.NAGAR,P.KERRY,P.MCEWAN, JRNL AUTH 2 H.SRINATH,K.CLANCY,S.PARELKAR,P.R.THOMPSON JRNL TITL DEVELOPMENT OF A SELECTIVE INHIBITOR OF PROTEIN ARGININE JRNL TITL 2 DEIMINASE 2. JRNL REF J. MED. CHEM. V. 60 3198 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28328217 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00274 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 37798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.29 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2051 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4998 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.43000 REMARK 3 B22 (A**2) : 8.75000 REMARK 3 B33 (A**2) : -1.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.60000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.230 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.195 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.749 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5171 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4764 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7023 ; 1.824 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11110 ; 1.054 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 633 ; 7.371 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;36.465 ;24.598 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 880 ;16.209 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;14.897 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 779 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5709 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1009 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2541 ; 3.772 ; 4.544 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2540 ; 3.772 ; 4.544 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3171 ; 5.620 ; 6.796 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3172 ; 5.620 ; 6.796 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2630 ; 4.422 ; 4.976 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2627 ; 4.424 ; 4.971 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3847 ; 6.711 ; 7.257 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 23151 ; 9.626 ;85.496 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 23152 ; 9.626 ;85.495 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5N0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41587 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.070 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.67 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 IMIDAZOLE PH7.5, 0.2MM LISO4, 8 REMARK 280 -11% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K 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 73.77800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.46450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.77800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.46450 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: 6240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -152.0 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 -6 REMARK 465 PRO A -5 REMARK 465 LEU A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 PRO A -1 REMARK 465 GLN A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER 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 LYS A 128 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 ASP A 135 REMARK 465 GLN A 136 REMARK 465 ARG A 218 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 123 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 205 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 205 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 VAL A 367 CB - CA - C ANGL. DEV. = -11.8 DEGREES REMARK 500 VAL A 392 CB - CA - C ANGL. DEV. = -12.4 DEGREES REMARK 500 ARG A 427 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 427 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 36 -18.93 86.23 REMARK 500 LEU A 70 66.35 -105.15 REMARK 500 GLU A 160 -80.14 -72.34 REMARK 500 GLN A 306 -32.86 -135.43 REMARK 500 LYS A 331 38.83 70.22 REMARK 500 LYS A 362 133.56 -178.81 REMARK 500 ARG A 374 -157.29 -97.71 REMARK 500 GLN A 455 -51.99 64.25 REMARK 500 ALA A 458 88.71 2.35 REMARK 500 ARG A 484 -126.00 52.50 REMARK 500 PHE A 515 10.89 82.19 REMARK 500 LYS A 574 -124.97 -134.37 REMARK 500 TYR A 636 -54.06 -120.91 REMARK 500 HIS A 640 31.83 70.33 REMARK 500 GLU A 642 -151.21 -127.88 REMARK 500 REMARK 500 REMARK: NULL 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 704 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 153 OD1 REMARK 620 2 ASP A 155 OD1 83.4 REMARK 620 3 ASP A 157 OD2 161.2 96.5 REMARK 620 4 ASP A 165 OD2 104.3 82.1 94.3 REMARK 620 5 ASP A 176 OD1 85.4 154.9 101.2 79.0 REMARK 620 6 ASP A 179 OD2 91.2 93.1 70.0 163.1 109.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 705 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 155 OD2 REMARK 620 2 ASP A 157 OD1 86.2 REMARK 620 3 ASP A 157 OD2 85.2 47.8 REMARK 620 4 ASP A 179 OD1 103.0 159.2 113.7 REMARK 620 5 ASP A 179 OD2 79.9 113.9 66.8 51.1 REMARK 620 6 ASP A 388 OD1 97.2 80.2 127.8 116.4 165.1 REMARK 620 7 HOH A 932 O 158.7 76.1 74.2 90.4 96.3 91.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 706 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 165 O REMARK 620 2 ASP A 168 OD1 88.2 REMARK 620 3 GLU A 170 O 173.7 86.0 REMARK 620 4 HOH A 970 O 83.4 94.0 94.6 REMARK 620 5 HOH A 804 O 85.6 66.8 94.2 158.1 REMARK 620 6 HOH A 845 O 87.0 148.1 99.2 116.8 81.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 349 OE1 REMARK 620 2 GLU A 353 OE1 134.3 REMARK 620 3 PHE A 407 O 89.5 98.5 REMARK 620 4 LEU A 410 O 147.4 78.0 78.9 REMARK 620 5 GLU A 411 OE1 82.0 136.2 106.5 72.5 REMARK 620 6 HOH A 893 O 95.9 76.1 174.1 97.6 76.5 REMARK 620 7 HOH A 827 O 68.3 70.1 76.3 135.7 150.3 103.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 703 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 351 OE1 REMARK 620 2 ASP A 369 OD1 106.1 REMARK 620 3 SER A 370 O 89.6 89.8 REMARK 620 4 ASN A 373 OD1 88.8 163.1 98.5 REMARK 620 5 HOH A 805 O 99.5 88.4 170.8 81.2 REMARK 620 6 HOH A 913 O 170.3 82.1 85.2 83.8 85.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 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 CA A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8FQ A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 708 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5N0M RELATED DB: PDB DBREF 5N0Y A 1 663 UNP Q9UM07 PADI4_HUMAN 1 663 SEQADV 5N0Y GLY A -6 UNP Q9UM07 EXPRESSION TAG SEQADV 5N0Y PRO A -5 UNP Q9UM07 EXPRESSION TAG SEQADV 5N0Y LEU A -4 UNP Q9UM07 EXPRESSION TAG SEQADV 5N0Y GLY A -3 UNP Q9UM07 EXPRESSION TAG SEQADV 5N0Y SER A -2 UNP Q9UM07 EXPRESSION TAG SEQADV 5N0Y PRO A -1 UNP Q9UM07 EXPRESSION TAG SEQADV 5N0Y GLN A 0 UNP Q9UM07 EXPRESSION TAG SEQADV 5N0Y SER A 55 UNP Q9UM07 GLY 55 ENGINEERED MUTATION SEQADV 5N0Y ALA A 82 UNP Q9UM07 VAL 82 ENGINEERED MUTATION SEQADV 5N0Y ALA A 112 UNP Q9UM07 GLY 112 ENGINEERED MUTATION SEQRES 1 A 670 GLY PRO LEU GLY SER PRO GLN MET ALA GLN GLY THR LEU SEQRES 2 A 670 ILE ARG VAL THR PRO GLU GLN PRO THR HIS ALA VAL CYS SEQRES 3 A 670 VAL LEU GLY THR LEU THR GLN LEU ASP ILE CYS SER SER SEQRES 4 A 670 ALA PRO GLU ASP CYS THR SER PHE SER ILE ASN ALA SER SEQRES 5 A 670 PRO GLY VAL VAL VAL ASP ILE ALA HIS SER PRO PRO ALA SEQRES 6 A 670 LYS LYS LYS SER THR GLY SER SER THR TRP PRO LEU ASP SEQRES 7 A 670 PRO GLY VAL GLU VAL THR LEU THR MET LYS ALA ALA SER SEQRES 8 A 670 GLY SER THR GLY ASP GLN LYS VAL GLN ILE SER TYR TYR SEQRES 9 A 670 GLY PRO LYS THR PRO PRO VAL LYS ALA LEU LEU TYR LEU SEQRES 10 A 670 THR ALA VAL GLU ILE SER LEU CYS ALA ASP ILE THR ARG SEQRES 11 A 670 THR GLY LYS VAL LYS PRO THR ARG ALA VAL LYS ASP GLN SEQRES 12 A 670 ARG THR TRP THR TRP GLY PRO CYS GLY GLN GLY ALA ILE SEQRES 13 A 670 LEU LEU VAL ASN CYS ASP ARG ASP ASN LEU GLU SER SER SEQRES 14 A 670 ALA MET ASP CYS GLU ASP ASP GLU VAL LEU ASP SER GLU SEQRES 15 A 670 ASP LEU GLN ASP MET SER LEU MET THR LEU SER THR LYS SEQRES 16 A 670 THR PRO LYS ASP PHE PHE THR ASN HIS THR LEU VAL LEU SEQRES 17 A 670 HIS VAL ALA ARG SER GLU MET ASP LYS VAL ARG VAL PHE SEQRES 18 A 670 GLN ALA THR ARG GLY LYS LEU SER SER LYS CYS SER VAL SEQRES 19 A 670 VAL LEU GLY PRO LYS TRP PRO SER HIS TYR LEU MET VAL SEQRES 20 A 670 PRO GLY GLY LYS HIS ASN MET ASP PHE TYR VAL GLU ALA SEQRES 21 A 670 LEU ALA PHE PRO ASP THR ASP PHE PRO GLY LEU ILE THR SEQRES 22 A 670 LEU THR ILE SER LEU LEU ASP THR SER ASN LEU GLU LEU SEQRES 23 A 670 PRO GLU ALA VAL VAL PHE GLN ASP SER VAL VAL PHE ARG SEQRES 24 A 670 VAL ALA PRO TRP ILE MET THR PRO ASN THR GLN PRO PRO SEQRES 25 A 670 GLN GLU VAL TYR ALA CYS SER ILE PHE GLU ASN GLU ASP SEQRES 26 A 670 PHE LEU LYS SER VAL THR THR LEU ALA MET LYS ALA LYS SEQRES 27 A 670 CYS LYS LEU THR ILE CYS PRO GLU GLU GLU ASN MET ASP SEQRES 28 A 670 ASP GLN TRP MET GLN ASP GLU MET GLU ILE GLY TYR ILE SEQRES 29 A 670 GLN ALA PRO HIS LYS THR LEU PRO VAL VAL PHE ASP SER SEQRES 30 A 670 PRO ARG ASN ARG GLY LEU LYS GLU PHE PRO ILE LYS ARG SEQRES 31 A 670 VAL MET GLY PRO ASP PHE GLY TYR VAL THR ARG GLY PRO SEQRES 32 A 670 GLN THR GLY GLY ILE SER GLY LEU ASP SER PHE GLY ASN SEQRES 33 A 670 LEU GLU VAL SER PRO PRO VAL THR VAL ARG GLY LYS GLU SEQRES 34 A 670 TYR PRO LEU GLY ARG ILE LEU PHE GLY ASP SER CYS TYR SEQRES 35 A 670 PRO SER ASN ASP SER ARG GLN MET HIS GLN ALA LEU GLN SEQRES 36 A 670 ASP PHE LEU SER ALA GLN GLN VAL GLN ALA PRO VAL LYS SEQRES 37 A 670 LEU TYR SER ASP TRP LEU SER VAL GLY HIS VAL ASP GLU SEQRES 38 A 670 PHE LEU SER PHE VAL PRO ALA PRO ASP ARG LYS GLY PHE SEQRES 39 A 670 ARG LEU LEU LEU ALA SER PRO ARG SER CYS TYR LYS LEU SEQRES 40 A 670 PHE GLN GLU GLN GLN ASN GLU GLY HIS GLY GLU ALA LEU SEQRES 41 A 670 LEU PHE GLU GLY ILE LYS LYS LYS LYS GLN GLN LYS ILE SEQRES 42 A 670 LYS ASN ILE LEU SER ASN LYS THR LEU ARG GLU HIS ASN SEQRES 43 A 670 SER PHE VAL GLU ARG CYS ILE ASP TRP ASN ARG GLU LEU SEQRES 44 A 670 LEU LYS ARG GLU LEU GLY LEU ALA GLU SER ASP ILE ILE SEQRES 45 A 670 ASP ILE PRO GLN LEU PHE LYS LEU LYS GLU PHE SER LYS SEQRES 46 A 670 ALA GLU ALA PHE PHE PRO ASN MET VAL ASN MET LEU VAL SEQRES 47 A 670 LEU GLY LYS HIS LEU GLY ILE PRO LYS PRO PHE GLY PRO SEQRES 48 A 670 VAL ILE ASN GLY ARG CYS CYS LEU GLU GLU LYS VAL CYS SEQRES 49 A 670 SER LEU LEU GLU PRO LEU GLY LEU GLN CYS THR PHE ILE SEQRES 50 A 670 ASN ASP PHE PHE THR TYR HIS ILE ARG HIS GLY GLU VAL SEQRES 51 A 670 HIS CYS GLY THR ASN VAL ARG ARG LYS PRO PHE SER PHE SEQRES 52 A 670 LYS TRP TRP ASN MET VAL PRO HET SO4 A 701 5 HET CA A 702 1 HET CA A 703 1 HET CA A 704 1 HET CA A 705 1 HET CA A 706 1 HET 8FQ A 707 33 HET SO4 A 708 5 HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION HETNAM 8FQ ~{N}-[(1~{S})-4-(2-FLUORANYLETHANIMIDOYLAMINO)-1-(4- HETNAM 2 8FQ METHOXY-1-METHYL-BENZIMIDAZOL-2-YL)BUTYL]-3- HETNAM 3 8FQ OXIDANYLIDENE-1,2-DIHYDROISOINDOLE-4-CARBOXAMIDE FORMUL 2 SO4 2(O4 S 2-) FORMUL 3 CA 5(CA 2+) FORMUL 8 8FQ C24 H27 F N6 O3 FORMUL 10 HOH *238(H2 O) HELIX 1 AA1 MET A 164 ASP A 168 5 5 HELIX 2 AA2 GLU A 175 MET A 180 5 6 HELIX 3 AA3 ASP A 192 ASN A 196 1 5 HELIX 4 AA4 GLU A 207 ASP A 209 5 3 HELIX 5 AA5 ASN A 316 ALA A 330 1 15 HELIX 6 AA6 PRO A 338 MET A 343 1 6 HELIX 7 AA7 GLU A 378 VAL A 384 1 7 HELIX 8 AA8 SER A 402 GLY A 408 5 7 HELIX 9 AA9 HIS A 444 GLN A 454 1 11 HELIX 10 AB1 HIS A 471 GLU A 474 5 4 HELIX 11 AB2 PRO A 494 GLU A 507 1 14 HELIX 12 AB3 ILE A 526 SER A 531 1 6 HELIX 13 AB4 ASN A 532 GLY A 558 1 27 HELIX 14 AB5 ALA A 560 SER A 562 5 3 HELIX 15 AB6 GLU A 575 SER A 577 5 3 HELIX 16 AB7 CYS A 611 GLU A 621 1 11 HELIX 17 AB8 PRO A 622 GLY A 624 5 3 HELIX 18 AB9 TYR A 636 HIS A 640 5 5 HELIX 19 AC1 VAL A 643 CYS A 645 5 3 HELIX 20 AC2 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 GLU A 75 MET A 80 -1 O VAL A 76 N LEU A 27 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 THR A 101 ALA A 119 1 O TYR A 109 N THR A 15 SHEET 3 AA2 5 GLN A 90 GLY A 98 -1 N ILE A 94 O ALA A 106 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 THR A 101 ALA A 119 1 O TYR A 109 N THR A 15 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 MET A 247 N LEU A 185 SHEET 5 AA3 6 VAL A 211 ALA A 216 -1 N PHE A 214 O TYR A 250 SHEET 6 AA3 6 SER A 226 LEU A 229 -1 O SER A 226 N GLN A 215 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 265 O PHE A 291 SHEET 4 AA4 5 HIS A 197 HIS A 202 -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 CYS A 337 0 SHEET 2 AA5 3 PRO A 305 CYS A 311 1 N ALA A 310 O CYS A 337 SHEET 3 AA5 3 THR A 647 ARG A 651 -1 O ASN A 648 N TYR A 309 SHEET 1 AA6 3 MET A 352 ALA A 359 0 SHEET 2 AA6 3 LYS A 362 ASP A 369 -1 O PHE A 368 N GLU A 353 SHEET 3 AA6 3 GLY A 390 THR A 393 1 O GLY A 390 N PRO A 365 SHEET 1 AA7 3 LEU A 410 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 TYR A 423 N VAL A 416 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 GLN A 626 N LEU A 596 SHEET 1 AB4 2 VAL A 605 ILE A 606 0 SHEET 2 AB4 2 ARG A 609 CYS A 610 -1 O ARG A 609 N ILE A 606 LINK OD1 ASN A 153 CA CA A 704 1555 1555 2.46 LINK OD1 ASP A 155 CA CA A 704 1555 1555 2.44 LINK OD2 ASP A 155 CA CA A 705 1555 1555 2.46 LINK OD1 ASP A 157 CA CA A 705 1555 1555 2.86 LINK OD2 ASP A 157 CA CA A 705 1555 1555 2.46 LINK OD2 ASP A 157 CA CA A 704 1555 1555 2.58 LINK O ASP A 165 CA CA A 706 1555 1555 2.29 LINK OD2 ASP A 165 CA CA A 704 1555 1555 2.03 LINK OD1 ASP A 168 CA CA A 706 1555 1555 2.17 LINK O GLU A 170 CA CA A 706 1555 1555 2.21 LINK OD1 ASP A 176 CA CA A 704 1555 1555 2.42 LINK OD1 ASP A 179 CA CA A 705 1555 1555 2.58 LINK OD2 ASP A 179 CA CA A 705 1555 1555 2.51 LINK OD2 ASP A 179 CA CA A 704 1555 1555 2.15 LINK OE1 GLN A 349 CA CA A 702 1555 1555 2.37 LINK OE1 GLU A 351 CA CA A 703 1555 1555 2.46 LINK OE1 GLU A 353 CA CA A 702 1555 1555 2.45 LINK OD1 ASP A 369 CA CA A 703 1555 1555 2.22 LINK O SER A 370 CA CA A 703 1555 1555 2.28 LINK OD1 ASN A 373 CA CA A 703 1555 1555 2.41 LINK OD1 ASP A 388 CA CA A 705 1555 1555 2.26 LINK O PHE A 407 CA CA A 702 1555 1555 2.27 LINK O LEU A 410 CA CA A 702 1555 1555 2.52 LINK OE1 GLU A 411 CA CA A 702 1555 1555 2.41 LINK SG CYS A 645 C14 8FQ A 707 1555 1555 1.69 LINK CA CA A 702 O HOH A 893 1555 1555 2.56 LINK CA CA A 702 O HOH A 827 1555 1555 2.62 LINK CA CA A 703 O HOH A 805 1555 1555 2.35 LINK CA CA A 703 O HOH A 913 1555 1555 2.47 LINK CA CA A 705 O HOH A 932 1555 1555 2.21 LINK CA CA A 706 O HOH A 970 1555 1555 2.34 LINK CA CA A 706 O HOH A 804 1555 1555 2.44 LINK CA CA A 706 O HOH A 845 1555 1555 2.35 SITE 1 AC1 5 SER A 402 GLY A 403 ARG A 441 8FQ A 707 SITE 2 AC1 5 HOH A 834 SITE 1 AC2 7 GLN A 349 GLU A 353 PHE A 407 LEU A 410 SITE 2 AC2 7 GLU A 411 HOH A 827 HOH A 893 SITE 1 AC3 6 GLU A 351 ASP A 369 SER A 370 ASN A 373 SITE 2 AC3 6 HOH A 805 HOH A 913 SITE 1 AC4 6 ASN A 153 ASP A 155 ASP A 157 ASP A 165 SITE 2 AC4 6 ASP A 176 ASP A 179 SITE 1 AC5 5 ASP A 155 ASP A 157 ASP A 179 ASP A 388 SITE 2 AC5 5 HOH A 932 SITE 1 AC6 6 ASP A 165 ASP A 168 GLU A 170 HOH A 804 SITE 2 AC6 6 HOH A 845 HOH A 970 SITE 1 AC7 13 TRP A 347 ASP A 350 ARG A 374 VAL A 469 SITE 2 AC7 13 HIS A 471 ASP A 473 ARG A 639 HIS A 640 SITE 3 AC7 13 CYS A 645 SO4 A 701 HOH A 803 HOH A 870 SITE 4 AC7 13 HOH A 878 SITE 1 AC8 3 LYS A 525 LYS A 527 ASN A 528 CRYST1 147.556 60.929 115.656 90.00 124.69 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 0.006777 0.000000 0.004691 0.00000 SCALE2 0.000000 0.016413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010516 0.00000