PDB Short entry for 4DKT HEADER HYDROLASE/HYDROLASE INHIBITOR 04-FEB-12 4DKT TITLE CRYSTAL STRUCTURE OF HUMAN PEPTIDYLARGININE DEIMINASE 4 IN COMPLEX TITLE 2 WITH N-ACETYL-L-THREONYL-L-ALPHA-ASPARTYL-N5-[(1E)-2- TITLE 3 FLUOROETHANIMIDOYL]-L-ORNITHINAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-ARGININE DEIMINASE TYPE-4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN ARGININE DEIMINASE 4, HL-60 PAD, PEPTIDYLARGININE COMPND 5 DEIMINASE IV, PROTEIN-ARGININE DEIMINASE TYPE IV; COMPND 6 EC: 3.5.3.15; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: THR-ASP-F-AMIDINE; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: N-ACETYL-L-THREONYL-L-ALPHA-ASPARTYL-N5-[(1E)-2- COMPND 12 FLUOROETHANIMIDOYL]-L-ORNITHINAMIDE, TDFA; COMPND 13 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS ALPHA/BETA-PROPELLER, IMMUNOGLOBULIN-LIKE, ARGININE CITRULLINATION, KEYWDS 2 POST-TRANSLATIONAL, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.E.JONES,J.L.SLACK,P.FANG,X.ZHANG,V.SUBRAMANIAN,C.P.CAUSEY, AUTHOR 2 S.A.COONROD,M.GUO,P.R.THOMPSON REVDAT 4 15-NOV-23 4DKT 1 LINK ATOM REVDAT 3 13-SEP-23 4DKT 1 REMARK SEQADV LINK REVDAT 2 15-NOV-17 4DKT 1 REMARK REVDAT 1 29-FEB-12 4DKT 0 JRNL AUTH J.E.JONES,J.L.SLACK,P.FANG,X.ZHANG,V.SUBRAMANIAN,C.P.CAUSEY, JRNL AUTH 2 S.A.COONROD,M.GUO,P.R.THOMPSON JRNL TITL SYNTHESIS AND SCREENING OF A HALOACETAMIDINE CONTAINING JRNL TITL 2 LIBRARY TO IDENTIFY PAD4 SELECTIVE INHIBITORS. JRNL REF ACS CHEM.BIOL. V. 7 160 2012 JRNL REFN ISSN 1554-8929 JRNL PMID 22004374 JRNL DOI 10.1021/CB200258Q REMARK 2 REMARK 2 RESOLUTION. 2.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 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) : 2.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 16858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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 41.4456 - 5.4118 1.00 2867 136 0.2036 0.2162 REMARK 3 2 5.4118 - 4.2969 1.00 2785 158 0.1576 0.2015 REMARK 3 3 4.2969 - 3.7542 1.00 2774 148 0.1690 0.2082 REMARK 3 4 3.7542 - 3.4111 1.00 2748 154 0.1927 0.2641 REMARK 3 5 3.4111 - 3.1667 0.98 2697 146 0.2216 0.2512 REMARK 3 6 3.1667 - 2.9800 0.77 2127 118 0.2505 0.2959 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 12.89 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.840 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23300 REMARK 3 B22 (A**2) : 5.48470 REMARK 3 B33 (A**2) : -4.25170 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.83400 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 5150 REMARK 3 ANGLE : 1.049 6988 REMARK 3 CHIRALITY : 0.073 779 REMARK 3 PLANARITY : 0.005 904 REMARK 3 DIHEDRAL : 15.665 1914 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4DKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G 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 : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 REMARK 200 STARTING MODEL: PDB ENTRY 1WDA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE, PH 8.0, 0.2 M LITHIUM REMARK 280 SULFATE, 10% W/V PEG1500, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 73.82700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.53950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.82700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.53950 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 THR-ASP-F-AMIDINE IS AN N-TERMINALLY ACETYLATED, C-TERMINALLY REMARK 400 AMIDATED TRIPEPTIDE. REMARK 400 REMARK 400 THE THR-ASP-F-AMIDINE IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: THR-ASP-F-AMIDINE REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 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 ARG A 131 REMARK 465 ALA A 132 REMARK 465 VAL A 133 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 465 SER A 312 REMARK 465 ILE A 313 REMARK 465 PHE A 314 REMARK 465 GLU A 315 REMARK 465 ASN A 316 REMARK 465 ACE B 1 REMARK 465 THR B 2 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 SER A 66 OG REMARK 470 LYS A 521 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 ASP A 36 -2.84 71.56 REMARK 500 ASP A 169 -1.11 89.72 REMARK 500 VAL A 228 -59.36 -124.68 REMARK 500 GLN A 306 -60.40 -127.89 REMARK 500 ASP A 344 -5.42 88.01 REMARK 500 ASN A 373 71.40 54.42 REMARK 500 ARG A 374 -82.76 -112.69 REMARK 500 LYS A 382 -69.53 -120.18 REMARK 500 GLN A 397 -15.23 70.66 REMARK 500 TYR A 423 75.98 -119.03 REMARK 500 GLN A 455 -20.79 72.09 REMARK 500 ARG A 484 -125.84 54.36 REMARK 500 LYS A 521 162.13 178.98 REMARK 500 LYS A 574 -80.27 -122.98 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 702 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 155 OD1 REMARK 620 2 ASP A 157 OD2 86.2 REMARK 620 3 ASP A 165 OD2 91.1 91.8 REMARK 620 4 ASP A 176 OD1 159.9 109.1 75.9 REMARK 620 5 ASP A 179 OD2 96.2 84.9 171.7 97.9 REMARK 620 N 1 2 3 4 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 ASP A 155 OD2 REMARK 620 2 ASP A 157 OD2 78.2 REMARK 620 3 GLU A 175 OE1 139.3 61.2 REMARK 620 4 GLU A 175 OE2 167.5 101.5 42.8 REMARK 620 5 ASP A 179 OD2 81.6 87.7 94.1 110.8 REMARK 620 6 ASP A 179 OD1 111.7 126.4 92.2 78.6 46.0 REMARK 620 7 ASP A 388 OD1 99.3 134.6 110.2 71.8 137.3 97.0 REMARK 620 N 1 2 3 4 5 6 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 168 OD2 REMARK 620 2 ASP A 176 OD2 117.6 REMARK 620 N 1 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 GLN A 349 OE1 REMARK 620 2 GLU A 353 OE1 137.6 REMARK 620 3 PHE A 407 O 61.0 98.5 REMARK 620 4 LEU A 410 O 121.0 77.3 69.5 REMARK 620 5 GLU A 411 OE1 77.5 140.7 83.6 66.7 REMARK 620 N 1 2 3 4 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 GLU A 351 OE1 REMARK 620 2 ASP A 369 OD2 131.7 REMARK 620 3 ASP A 369 OD1 86.4 46.7 REMARK 620 4 SER A 370 O 62.5 112.1 82.5 REMARK 620 5 ASN A 373 OD1 73.2 155.1 155.8 76.6 REMARK 620 N 1 2 3 4 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 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 SO4 A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF THR-ASP-F-AMIDINE DBREF 4DKT A 1 663 UNP Q9UM07 PADI4_HUMAN 1 663 DBREF 4DKT B 1 5 PDB 4DKT 4DKT 1 5 SEQADV 4DKT GLY A -4 UNP Q9UM07 EXPRESSION TAG SEQADV 4DKT PRO A -3 UNP Q9UM07 EXPRESSION TAG SEQADV 4DKT LEU A -2 UNP Q9UM07 EXPRESSION TAG SEQADV 4DKT GLY A -1 UNP Q9UM07 EXPRESSION TAG SEQADV 4DKT SER A 0 UNP Q9UM07 EXPRESSION TAG SEQADV 4DKT SER A 55 UNP Q9UM07 GLY 55 CONFLICT SEQADV 4DKT ALA A 82 UNP Q9UM07 VAL 82 CONFLICT SEQADV 4DKT ALA A 112 UNP Q9UM07 GLY 112 CONFLICT SEQRES 1 A 668 GLY PRO LEU GLY SER MET ALA GLN GLY THR LEU ILE ARG SEQRES 2 A 668 VAL THR PRO GLU GLN PRO THR HIS ALA VAL CYS VAL LEU SEQRES 3 A 668 GLY THR LEU THR GLN LEU ASP ILE CYS SER SER ALA PRO SEQRES 4 A 668 GLU ASP CYS THR SER PHE SER ILE ASN ALA SER PRO GLY SEQRES 5 A 668 VAL VAL VAL ASP ILE ALA HIS SER PRO PRO ALA LYS LYS SEQRES 6 A 668 LYS SER THR GLY SER SER THR TRP PRO LEU ASP PRO GLY SEQRES 7 A 668 VAL GLU VAL THR LEU THR MET LYS ALA ALA SER GLY SER SEQRES 8 A 668 THR GLY ASP GLN LYS VAL GLN ILE SER TYR TYR GLY PRO SEQRES 9 A 668 LYS THR PRO PRO VAL LYS ALA LEU LEU TYR LEU THR ALA SEQRES 10 A 668 VAL GLU ILE SER LEU CYS ALA ASP ILE THR ARG THR GLY SEQRES 11 A 668 LYS VAL LYS PRO THR ARG ALA VAL LYS ASP GLN ARG THR SEQRES 12 A 668 TRP THR TRP GLY PRO CYS GLY GLN GLY ALA ILE LEU LEU SEQRES 13 A 668 VAL ASN CYS ASP ARG ASP ASN LEU GLU SER SER ALA MET SEQRES 14 A 668 ASP CYS GLU ASP ASP GLU VAL LEU ASP SER GLU ASP LEU SEQRES 15 A 668 GLN ASP MET SER LEU MET THR LEU SER THR LYS THR PRO SEQRES 16 A 668 LYS ASP PHE PHE THR ASN HIS THR LEU VAL LEU HIS VAL SEQRES 17 A 668 ALA ARG SER GLU MET ASP LYS VAL ARG VAL PHE GLN ALA SEQRES 18 A 668 THR ARG GLY LYS LEU SER SER LYS CYS SER VAL VAL LEU SEQRES 19 A 668 GLY PRO LYS TRP PRO SER HIS TYR LEU MET VAL PRO GLY SEQRES 20 A 668 GLY LYS HIS ASN MET ASP PHE TYR VAL GLU ALA LEU ALA SEQRES 21 A 668 PHE PRO ASP THR ASP PHE PRO GLY LEU ILE THR LEU THR SEQRES 22 A 668 ILE SER LEU LEU ASP THR SER ASN LEU GLU LEU PRO GLU SEQRES 23 A 668 ALA VAL VAL PHE GLN ASP SER VAL VAL PHE ARG VAL ALA SEQRES 24 A 668 PRO TRP ILE MET THR PRO ASN THR GLN PRO PRO GLN GLU SEQRES 25 A 668 VAL TYR ALA CYS SER ILE PHE GLU ASN GLU ASP PHE LEU SEQRES 26 A 668 LYS SER VAL THR THR LEU ALA MET LYS ALA LYS CYS LYS SEQRES 27 A 668 LEU THR ILE CYS PRO GLU GLU GLU ASN MET ASP ASP GLN SEQRES 28 A 668 TRP MET GLN ASP GLU MET GLU ILE GLY TYR ILE GLN ALA SEQRES 29 A 668 PRO HIS LYS THR LEU PRO VAL VAL PHE ASP SER PRO ARG SEQRES 30 A 668 ASN ARG GLY LEU LYS GLU PHE PRO ILE LYS ARG VAL MET SEQRES 31 A 668 GLY PRO ASP PHE GLY TYR VAL THR ARG GLY PRO GLN THR SEQRES 32 A 668 GLY GLY ILE SER GLY LEU ASP SER PHE GLY ASN LEU GLU SEQRES 33 A 668 VAL SER PRO PRO VAL THR VAL ARG GLY LYS GLU TYR PRO SEQRES 34 A 668 LEU GLY ARG ILE LEU PHE GLY ASP SER CYS TYR PRO SER SEQRES 35 A 668 ASN ASP SER ARG GLN MET HIS GLN ALA LEU GLN ASP PHE SEQRES 36 A 668 LEU SER ALA GLN GLN VAL GLN ALA PRO VAL LYS LEU TYR SEQRES 37 A 668 SER ASP TRP LEU SER VAL GLY HIS VAL ASP GLU PHE LEU SEQRES 38 A 668 SER PHE VAL PRO ALA PRO ASP ARG LYS GLY PHE ARG LEU SEQRES 39 A 668 LEU LEU ALA SER PRO ARG SER CYS TYR LYS LEU PHE GLN SEQRES 40 A 668 GLU GLN GLN ASN GLU GLY HIS GLY GLU ALA LEU LEU PHE SEQRES 41 A 668 GLU GLY ILE LYS LYS LYS LYS GLN GLN LYS ILE LYS ASN SEQRES 42 A 668 ILE LEU SER ASN LYS THR LEU ARG GLU HIS ASN SER PHE SEQRES 43 A 668 VAL GLU ARG CYS ILE ASP TRP ASN ARG GLU LEU LEU LYS SEQRES 44 A 668 ARG GLU LEU GLY LEU ALA GLU SER ASP ILE ILE ASP ILE SEQRES 45 A 668 PRO GLN LEU PHE LYS LEU LYS GLU PHE SER LYS ALA GLU SEQRES 46 A 668 ALA PHE PHE PRO ASN MET VAL ASN MET LEU VAL LEU GLY SEQRES 47 A 668 LYS HIS LEU GLY ILE PRO LYS PRO PHE GLY PRO VAL ILE SEQRES 48 A 668 ASN GLY ARG CYS CYS LEU GLU GLU LYS VAL CYS SER LEU SEQRES 49 A 668 LEU GLU PRO LEU GLY LEU GLN CYS THR PHE ILE ASN ASP SEQRES 50 A 668 PHE PHE THR TYR HIS ILE ARG HIS GLY GLU VAL HIS CYS SEQRES 51 A 668 GLY THR ASN VAL ARG ARG LYS PRO PHE SER PHE LYS TRP SEQRES 52 A 668 TRP ASN MET VAL PRO SEQRES 1 B 5 ACE THR ASP FIO NH2 MODRES 4DKT FIO B 4 ARG HET FIO B 4 11 HET NH2 B 5 1 HET CA A 701 1 HET CA A 702 1 HET CA A 703 1 HET CA A 704 1 HET CA A 705 1 HET SO4 A 706 5 HET SO4 A 707 5 HET EDO A 708 4 HET EDO A 709 4 HETNAM FIO N~5~-[(1E)-2-FLUOROETHANIMIDOYL]-L-ORNITHINE HETNAM NH2 AMINO GROUP HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 FIO C7 H14 F N3 O2 FORMUL 2 NH2 H2 N FORMUL 3 CA 5(CA 2+) FORMUL 8 SO4 2(O4 S 2-) FORMUL 10 EDO 2(C2 H6 O2) FORMUL 12 HOH *37(H2 O) HELIX 1 1 MET A 164 ASP A 168 5 5 HELIX 2 2 SER A 174 ASP A 179 5 6 HELIX 3 3 ASP A 192 ASN A 196 1 5 HELIX 4 4 GLU A 207 ASP A 209 5 3 HELIX 5 5 ASP A 318 ALA A 330 1 13 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 LYS A 377 ARG A 383 1 7 HELIX 9 9 SER A 406 GLY A 408 5 3 HELIX 10 10 HIS A 444 GLN A 455 1 12 HELIX 11 11 HIS A 471 PHE A 475 1 5 HELIX 12 12 PRO A 494 GLU A 507 1 14 HELIX 13 13 ILE A 526 SER A 531 1 6 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 VAL A 643 CYS A 645 5 3 HELIX 21 21 LYS A 657 MET A 661 5 5 SHEET 1 A 4 LEU A 6 ARG A 8 0 SHEET 2 A 4 THR A 25 ASP A 28 1 O ASP A 28 N ILE A 7 SHEET 3 A 4 GLU A 75 MET A 80 -1 O VAL A 76 N LEU A 27 SHEET 4 A 4 VAL A 48 ALA A 53 -1 N ALA A 53 O GLU A 75 SHEET 1 B 3 THR A 15 VAL A 20 0 SHEET 2 B 3 VAL A 104 ALA A 119 1 O TYR A 109 N THR A 15 SHEET 3 B 3 LYS A 128 PRO A 129 -1 O LYS A 128 N ALA A 119 SHEET 1 C 8 TRP A 68 PRO A 69 0 SHEET 2 C 8 SER A 39 ALA A 44 -1 N PHE A 40 O TRP A 68 SHEET 3 C 8 GLN A 90 TYR A 97 -1 O SER A 95 N SER A 41 SHEET 4 C 8 VAL A 104 ALA A 119 -1 O VAL A 104 N TYR A 96 SHEET 5 C 8 SER A 181 THR A 189 -1 O THR A 184 N CYS A 118 SHEET 6 C 8 GLY A 243 ALA A 253 -1 O HIS A 245 N THR A 187 SHEET 7 C 8 VAL A 211 ALA A 216 -1 N ALA A 216 O ASP A 248 SHEET 8 C 8 SER A 226 VAL A 227 -1 O SER A 226 N GLN A 215 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 ALA A 148 SHEET 3 D 5 LEU A 264 ASP A 273 -1 N ILE A 269 O ASP A 287 SHEET 4 D 5 HIS A 197 VAL A 203 -1 N VAL A 200 O SER A 270 SHEET 5 D 5 SER A 235 TYR A 237 -1 O HIS A 236 N LEU A 201 SHEET 1 E 3 LYS A 333 ILE A 336 0 SHEET 2 E 3 PRO A 305 ALA A 310 1 N VAL A 308 O LYS A 333 SHEET 3 E 3 THR A 647 ARG A 651 -1 O ASN A 648 N TYR A 309 SHEET 1 F 3 MET A 352 ALA A 359 0 SHEET 2 F 3 LYS A 362 ASP A 369 -1 O LYS A 362 N ALA A 359 SHEET 3 F 3 GLY A 390 THR A 393 1 O GLY A 390 N PRO A 365 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 VAL A 460 N ILE A 428 SHEET 1 H 2 VAL A 416 VAL A 418 0 SHEET 2 H 2 LYS A 421 TYR A 423 -1 O LYS A 421 N VAL A 418 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 567 N SER A 493 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 HIS A 595 N LEU A 592 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 C20 FIO B 4 1555 1555 1.79 LINK C ASP B 3 N FIO B 4 1555 1555 1.33 LINK C FIO B 4 N NH2 B 5 1555 1555 1.42 LINK OD1 ASP A 155 CA CA A 702 1555 1555 2.74 LINK OD2 ASP A 155 CA CA A 703 1555 1555 2.84 LINK OD2 ASP A 157 CA CA A 702 1555 1555 2.72 LINK OD2 ASP A 157 CA CA A 703 1555 1555 2.57 LINK OD2 ASP A 165 CA CA A 702 1555 1555 2.79 LINK OD2 ASP A 168 CA CA A 705 1555 1555 2.74 LINK OE1 GLU A 175 CA CA A 703 1555 1555 2.97 LINK OE2 GLU A 175 CA CA A 703 1555 1555 3.03 LINK OD1 ASP A 176 CA CA A 702 1555 1555 2.87 LINK OD2 ASP A 176 CA CA A 705 1555 1555 2.99 LINK OD2 ASP A 179 CA CA A 702 1555 1555 2.64 LINK OD2 ASP A 179 CA CA A 703 1555 1555 2.66 LINK OD1 ASP A 179 CA CA A 703 1555 1555 2.94 LINK OE1 GLN A 349 CA CA A 701 1555 1555 2.59 LINK OE1 GLU A 351 CA CA A 704 1555 1555 2.98 LINK OE1 GLU A 353 CA CA A 701 1555 1555 2.65 LINK OD2 ASP A 369 CA CA A 704 1555 1555 2.72 LINK OD1 ASP A 369 CA CA A 704 1555 1555 2.85 LINK O SER A 370 CA CA A 704 1555 1555 2.73 LINK OD1 ASN A 373 CA CA A 704 1555 1555 2.55 LINK OD1 ASP A 388 CA CA A 703 1555 1555 2.56 LINK O PHE A 407 CA CA A 701 1555 1555 2.94 LINK O LEU A 410 CA CA A 701 1555 1555 2.76 LINK OE1 GLU A 411 CA CA A 701 1555 1555 2.90 SITE 1 AC1 5 GLN A 349 GLU A 353 PHE A 407 LEU A 410 SITE 2 AC1 5 GLU A 411 SITE 1 AC2 6 ASN A 153 ASP A 155 ASP A 157 ASP A 165 SITE 2 AC2 6 ASP A 176 ASP A 179 SITE 1 AC3 5 ASP A 155 ASP A 157 GLU A 175 ASP A 179 SITE 2 AC3 5 ASP A 388 SITE 1 AC4 5 GLU A 351 ASP A 369 SER A 370 ASN A 373 SITE 2 AC4 5 GLN A 397 SITE 1 AC5 6 ASP A 165 ASP A 168 GLU A 170 ASP A 176 SITE 2 AC5 6 MET A 180 GLU A 252 SITE 1 AC6 3 SER A 402 GLY A 403 ARG A 441 SITE 1 AC7 3 LYS A 525 LYS A 527 ASN A 528 SITE 1 AC8 4 ASP A 432 SER A 433 LYS A 461 LEU A 462 SITE 1 AC9 12 GLN A 346 TRP A 347 ASP A 350 ARG A 374 SITE 2 AC9 12 HIS A 471 ASP A 473 ASN A 588 ARG A 639 SITE 3 AC9 12 HIS A 640 GLY A 641 CYS A 645 HOH B 801 CRYST1 147.654 61.079 115.382 90.00 124.54 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 0.006773 0.000000 0.004662 0.00000 SCALE2 0.000000 0.016372 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010521 0.00000