HEADER HYDROLASE/HYDROLASE INHIBITOR 13-JUL-11 3B1U TITLE CRYSTAL STRUCTURE OF HUMAN PEPTIDYLARGININE DEIMINASE 4 IN COMPLEX TITLE 2 WITH O-F-AMIDINE 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, PADI5, PDI5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS NUCLEI, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.P.CAUSEY,J.E.JONES,J.L.SLACK,D.KAMEI,L.E.JONES JR,V.SUBRAMANIAN, AUTHOR 2 B.KNUCKLEY,P.EBRAHIMI,A.A.CHUMANEVICH,Y.LUO,H.HASHIMOTO,T.SHIMIZU, AUTHOR 3 M.SATO,L.J.HOFSETH,P.R.THOMPSON REVDAT 2 01-NOV-23 3B1U 1 REMARK SEQADV LINK REVDAT 1 26-OCT-11 3B1U 0 JRNL AUTH C.P.CAUSEY,J.E.JONES,J.L.SLACK,D.KAMEI,L.E.JONES JR, JRNL AUTH 2 V.SUBRAMANIAN,B.KNUCKLEY,P.EBRAHIMI,A.A.CHUMANEVICH,Y.LUO, JRNL AUTH 3 H.HASHIMOTO,M.SATO,L.J.HOFSETH,P.R.THOMPSON JRNL TITL THE DEVELOPMENT OF JRNL TITL 2 N-ALPHA-(2-CARBOXYL)BENZOYL-N(5)-(2-FLUORO-1-IMINOETHYL) JRNL TITL 3 -L-ORNITHINE AMIDE (O-F-AMIDINE) AND JRNL TITL 4 N-ALPHA-(2-CARBOXYL)BENZOYL-N(5)-(2-CHLORO-1-IMINOETHYL) JRNL TITL 5 -L-ORNITHINE AMIDE (O-CL-AMIDINE) AS SECOND GENERATION JRNL TITL 6 PROTEIN ARGININE DEIMINASE (PAD) INHIBITORS JRNL REF J.MED.CHEM. V. 54 6919 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21882827 JRNL DOI 10.1021/JM2008985 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 42464 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2254 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2099 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4947 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 174 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.52000 REMARK 3 B22 (A**2) : 2.83000 REMARK 3 B33 (A**2) : -2.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.67000 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): 0.186 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.926 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5101 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3484 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6924 ; 0.887 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8529 ; 3.025 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 623 ; 5.551 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 222 ;34.774 ;24.595 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 870 ;13.767 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;13.693 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 769 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5587 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 980 ; 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): 3140 ; 0.261 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1251 ; 0.028 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5110 ; 0.485 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1961 ; 0.467 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1814 ; 0.794 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 4 A 663 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6400 -0.0905 -1.4464 REMARK 3 T TENSOR REMARK 3 T11: 0.0155 T22: 0.1634 REMARK 3 T33: 0.0669 T12: 0.0011 REMARK 3 T13: -0.0101 T23: -0.0571 REMARK 3 L TENSOR REMARK 3 L11: 1.3443 L22: 0.3138 REMARK 3 L33: 3.7817 L12: 0.0303 REMARK 3 L13: 1.3275 L23: -0.1877 REMARK 3 S TENSOR REMARK 3 S11: -0.0234 S12: -0.1512 S13: 0.1065 REMARK 3 S21: 0.0104 S22: -0.0364 S23: 0.1065 REMARK 3 S31: 0.0973 S32: -0.3990 S33: 0.0599 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3B1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000029972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44771 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1WDA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8, VAPOR DIFFUSION, HANGING DROP, 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 73.21100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.23400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.21100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.23400 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: 6100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -180.0 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 GLN A 3 REMARK 465 ASP A 36 REMARK 465 CYS A 37 REMARK 465 ALA A 53 REMARK 465 HIS A 54 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 SER A 66 REMARK 465 VAL A 127 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 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 465 LYS A 224 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 160 73.12 60.65 REMARK 500 ILE A 313 -154.05 -137.43 REMARK 500 PHE A 314 170.58 -39.30 REMARK 500 GLU A 315 82.84 -34.86 REMARK 500 ARG A 374 -152.75 -87.56 REMARK 500 ARG A 383 32.79 -143.19 REMARK 500 GLN A 455 -40.89 70.09 REMARK 500 ALA A 458 89.37 -1.47 REMARK 500 ARG A 484 -125.34 58.18 REMARK 500 LYS A 520 38.71 -96.53 REMARK 500 LYS A 574 -120.63 -125.62 REMARK 500 PRO A 584 121.64 -39.92 REMARK 500 ASN A 585 95.04 -67.03 REMARK 500 LEU A 592 76.97 -113.68 REMARK 500 GLU A 642 -153.10 -135.84 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 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 153 OD1 REMARK 620 2 ASP A 155 OD1 79.5 REMARK 620 3 ASP A 157 OD2 169.3 97.9 REMARK 620 4 ASP A 165 OD2 104.8 87.5 85.3 REMARK 620 5 ASP A 176 OD2 88.5 159.9 96.7 79.9 REMARK 620 6 ASP A 179 OD2 94.1 81.1 75.2 155.7 116.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 155 OD2 REMARK 620 2 ASP A 157 OD1 81.3 REMARK 620 3 ASP A 157 OD2 80.2 49.3 REMARK 620 4 ASP A 179 OD2 80.5 118.0 69.3 REMARK 620 5 ASP A 179 OD1 105.4 161.0 113.5 47.9 REMARK 620 6 ASP A 388 OD1 102.3 95.1 143.9 146.7 100.6 REMARK 620 7 HOH A 764 O 155.7 75.9 78.5 102.7 93.8 88.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 904 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 165 O REMARK 620 2 ASP A 168 OD2 77.6 REMARK 620 3 GLU A 170 O 163.6 86.3 REMARK 620 4 HOH A 753 O 85.1 150.1 108.4 REMARK 620 5 HOH A 788 O 81.9 79.2 92.7 74.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 900 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 349 OE1 REMARK 620 2 GLU A 353 OE1 133.9 REMARK 620 3 PHE A 407 O 90.9 97.0 REMARK 620 4 LEU A 410 O 148.1 78.0 83.4 REMARK 620 5 GLU A 411 OE1 80.3 140.7 102.0 70.4 REMARK 620 6 HOH A 778 O 67.6 69.2 80.0 140.8 147.8 REMARK 620 7 HOH A 781 O 90.1 78.7 174.8 98.4 83.2 95.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 901 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 351 OE1 REMARK 620 2 ASP A 369 OD1 96.4 REMARK 620 3 SER A 370 O 89.9 84.8 REMARK 620 4 ASN A 373 OD1 99.0 164.6 94.3 REMARK 620 5 HOH A 789 O 169.6 90.8 83.3 73.8 REMARK 620 6 HOH A 816 O 110.8 86.1 158.2 89.3 77.1 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 YFF A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 904 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B1T RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 G55S, V82A AND G112A ARE NATURAL VARIANTS BASED ON REF 1 AND 4 OF REMARK 999 DATABASE UNIPROT/SWISS-PROT Q9UM07 (PADI4_HUMAN). DBREF 3B1U A 1 663 UNP Q9UM07 PADI4_HUMAN 1 663 SEQADV 3B1U GLY A -7 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U PRO A -6 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U LEU A -5 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U GLY A -4 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U SER A -3 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U PRO A -2 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U GLU A -1 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U PHE A 0 UNP Q9UM07 EXPRESSION TAG SEQADV 3B1U SER A 55 UNP Q9UM07 GLY 55 SEE REMARK 999 SEQADV 3B1U ALA A 82 UNP Q9UM07 VAL 82 SEE REMARK 999 SEQADV 3B1U ALA A 112 UNP Q9UM07 GLY 112 SEE REMARK 999 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 SER 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 ALA 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 ALA 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 CYS GLY THR ASN VAL ARG ARG LYS PRO PHE SER SEQRES 52 A 671 PHE LYS TRP TRP ASN MET VAL PRO HET YFF A 800 23 HET SO4 A 905 5 HET SO4 A 906 5 HET SO4 A 907 5 HET CA A 900 1 HET CA A 901 1 HET CA A 902 1 HET CA A 903 1 HET CA A 904 1 HETNAM YFF 2-{[(2S)-1-AMINO-5-{[(1Z)-2-FLUOROETHANIMIDOYL]AMINO}- HETNAM 2 YFF 1-OXOPENTAN-2-YL]CARBAMOYL}BENZOIC ACID HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION HETSYN YFF O-F-AMIDINE FORMUL 2 YFF C15 H19 F N4 O4 FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 CA 5(CA 2+) FORMUL 11 HOH *174(H2 O) HELIX 1 1 MET A 164 ASP A 168 5 5 HELIX 2 2 SER A 174 MET A 180 5 7 HELIX 3 3 ASP A 192 THR A 195 5 4 HELIX 4 4 GLU A 207 ASP A 209 5 3 HELIX 5 5 ASN A 316 ALA A 330 1 15 HELIX 6 6 PRO A 338 MET A 343 1 6 HELIX 7 7 TRP A 347 GLU A 351 1 5 HELIX 8 8 GLU A 378 VAL A 384 1 7 HELIX 9 9 SER A 402 GLY A 408 5 7 HELIX 10 10 HIS A 444 GLN A 454 1 11 HELIX 11 11 HIS A 471 GLU A 474 5 4 HELIX 12 12 PRO A 494 GLU A 507 1 14 HELIX 13 13 ILE A 526 ASN A 532 1 7 HELIX 14 14 ASN A 532 GLY A 558 1 27 HELIX 15 15 ALA A 560 SER A 562 5 3 HELIX 16 16 GLU A 575 SER A 577 5 3 HELIX 17 17 CYS A 611 GLU A 621 1 11 HELIX 18 18 PRO A 622 GLY A 624 5 3 HELIX 19 19 TYR A 636 HIS A 640 5 5 HELIX 20 20 LYS A 657 MET A 661 5 5 SHEET 1 A 4 THR A 5 ARG A 8 0 SHEET 2 A 4 THR A 25 ASP A 28 1 O GLN A 26 N ILE A 7 SHEET 3 A 4 VAL A 76 MET A 80 -1 O LEU A 78 N THR A 25 SHEET 4 A 4 VAL A 48 ASP A 51 -1 N ASP A 51 O THR A 77 SHEET 1 B 5 THR A 15 VAL A 20 0 SHEET 2 B 5 VAL A 104 CYS A 118 1 O TYR A 109 N THR A 15 SHEET 3 B 5 GLN A 90 TYR A 97 -1 N TYR A 96 O VAL A 104 SHEET 4 B 5 SER A 39 ALA A 44 -1 N SER A 41 O SER A 95 SHEET 5 B 5 TRP A 68 PRO A 69 -1 O TRP A 68 N PHE A 40 SHEET 1 C 6 THR A 15 VAL A 20 0 SHEET 2 C 6 VAL A 104 CYS A 118 1 O TYR A 109 N THR A 15 SHEET 3 C 6 SER A 181 LYS A 188 -1 O THR A 184 N CYS A 118 SHEET 4 C 6 LYS A 244 ALA A 253 -1 O PHE A 249 N MET A 183 SHEET 5 C 6 VAL A 211 GLN A 215 -1 N PHE A 214 O TYR A 250 SHEET 6 C 6 SER A 226 LEU A 229 -1 O LEU A 229 N VAL A 213 SHEET 1 D 5 ALA A 148 LEU A 150 0 SHEET 2 D 5 ALA A 282 VAL A 293 1 O ARG A 292 N LEU A 150 SHEET 3 D 5 LEU A 264 ASP A 273 -1 N ILE A 265 O PHE A 291 SHEET 4 D 5 HIS A 197 HIS A 202 -1 N THR A 198 O LEU A 272 SHEET 5 D 5 SER A 235 LEU A 238 -1 O LEU A 238 N LEU A 199 SHEET 1 E 3 LYS A 333 CYS A 337 0 SHEET 2 E 3 PRO A 305 CYS A 311 1 N ALA A 310 O CYS A 337 SHEET 3 E 3 THR A 647 ARG A 651 -1 O ARG A 650 N GLN A 306 SHEET 1 F 3 MET A 352 GLN A 358 0 SHEET 2 F 3 THR A 363 ASP A 369 -1 O PHE A 368 N GLU A 353 SHEET 3 F 3 GLY A 390 THR A 393 1 O VAL A 392 N ASP A 369 SHEET 1 G 3 LEU A 410 VAL A 412 0 SHEET 2 G 3 ILE A 428 ASP A 432 -1 O LEU A 429 N GLU A 411 SHEET 3 G 3 VAL A 460 TYR A 463 1 O LEU A 462 N PHE A 430 SHEET 1 H 2 VAL A 416 VAL A 418 0 SHEET 2 H 2 LYS A 421 TYR A 423 -1 O TYR A 423 N VAL A 416 SHEET 1 I 3 LEU A 476 PRO A 480 0 SHEET 2 I 3 PHE A 487 SER A 493 -1 O LEU A 490 N SER A 477 SHEET 3 I 3 ILE A 564 PRO A 568 1 O ILE A 565 N LEU A 489 SHEET 1 J 2 LEU A 513 LEU A 514 0 SHEET 2 J 2 GLN A 524 LYS A 525 -1 O GLN A 524 N LEU A 514 SHEET 1 K 2 PHE A 571 LEU A 573 0 SHEET 2 K 2 ALA A 579 ALA A 581 -1 O GLU A 580 N LYS A 572 SHEET 1 L 3 LEU A 590 LEU A 592 0 SHEET 2 L 3 HIS A 595 PRO A 599 -1 O GLY A 597 N LEU A 590 SHEET 3 L 3 GLN A 626 ILE A 630 1 O GLN A 626 N LEU A 596 SHEET 1 M 2 VAL A 605 ILE A 606 0 SHEET 2 M 2 ARG A 609 CYS A 610 -1 O ARG A 609 N ILE A 606 LINK SG CYS A 645 CAP YFF A 800 1555 1555 1.80 LINK OD1 ASN A 153 CA CA A 902 1555 1555 2.41 LINK OD1 ASP A 155 CA CA A 902 1555 1555 2.39 LINK OD2 ASP A 155 CA CA A 903 1555 1555 2.44 LINK OD2 ASP A 157 CA CA A 902 1555 1555 2.42 LINK OD1 ASP A 157 CA CA A 903 1555 1555 2.63 LINK OD2 ASP A 157 CA CA A 903 1555 1555 2.63 LINK OD2 ASP A 165 CA CA A 902 1555 1555 2.46 LINK O ASP A 165 CA CA A 904 1555 1555 2.33 LINK OD2 ASP A 168 CA CA A 904 1555 1555 2.42 LINK O GLU A 170 CA CA A 904 1555 1555 2.29 LINK OD2 ASP A 176 CA CA A 902 1555 1555 2.34 LINK OD2 ASP A 179 CA CA A 902 1555 1555 2.33 LINK OD2 ASP A 179 CA CA A 903 1555 1555 2.45 LINK OD1 ASP A 179 CA CA A 903 1555 1555 2.86 LINK OE1 GLN A 349 CA CA A 900 1555 1555 2.31 LINK OE1 GLU A 351 CA CA A 901 1555 1555 2.33 LINK OE1 GLU A 353 CA CA A 900 1555 1555 2.40 LINK OD1 ASP A 369 CA CA A 901 1555 1555 2.46 LINK O SER A 370 CA CA A 901 1555 1555 2.24 LINK OD1 ASN A 373 CA CA A 901 1555 1555 2.32 LINK OD1 ASP A 388 CA CA A 903 1555 1555 2.25 LINK O PHE A 407 CA CA A 900 1555 1555 2.25 LINK O LEU A 410 CA CA A 900 1555 1555 2.46 LINK OE1 GLU A 411 CA CA A 900 1555 1555 2.61 LINK O HOH A 753 CA CA A 904 1555 1555 2.30 LINK O HOH A 764 CA CA A 903 1555 1555 2.27 LINK O HOH A 778 CA CA A 900 1555 1555 2.57 LINK O HOH A 781 CA CA A 900 1555 1555 2.34 LINK O HOH A 788 CA CA A 904 1555 1555 2.44 LINK O HOH A 789 CA CA A 901 1555 1555 2.48 LINK O HOH A 816 CA CA A 901 1555 1555 2.33 SITE 1 AC1 12 TRP A 347 ASP A 350 ARG A 374 VAL A 469 SITE 2 AC1 12 HIS A 471 ASP A 473 ASN A 588 ARG A 639 SITE 3 AC1 12 HIS A 640 CYS A 645 HOH A 759 HOH A 763 SITE 1 AC2 2 GLY A 403 ARG A 441 SITE 1 AC3 5 ARG A 495 SER A 496 LYS A 499 LYS A 615 SITE 2 AC3 5 HOH A 738 SITE 1 AC4 3 GLU A 516 LYS A 525 ASN A 528 SITE 1 AC5 7 GLN A 349 GLU A 353 PHE A 407 LEU A 410 SITE 2 AC5 7 GLU A 411 HOH A 778 HOH A 781 SITE 1 AC6 6 GLU A 351 ASP A 369 SER A 370 ASN A 373 SITE 2 AC6 6 HOH A 789 HOH A 816 SITE 1 AC7 6 ASN A 153 ASP A 155 ASP A 157 ASP A 165 SITE 2 AC7 6 ASP A 176 ASP A 179 SITE 1 AC8 5 ASP A 155 ASP A 157 ASP A 179 ASP A 388 SITE 2 AC8 5 HOH A 764 SITE 1 AC9 5 ASP A 165 ASP A 168 GLU A 170 HOH A 753 SITE 2 AC9 5 HOH A 788 CRYST1 146.422 60.468 115.506 90.00 124.43 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 0.006830 0.000000 0.004682 0.00000 SCALE2 0.000000 0.016538 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010497 0.00000