HEADER HYDROLASE/HYDROLASE INHIBITOR 16-JUN-04 1TQ7 TITLE CRYSTAL STRUCTURE OF THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A TITLE 2 BOUND TO PPACK COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGHT CHAIN; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROTHROMBIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: HEAVY CHAIN; COMPND 12 SYNONYM: COAGULATION FACTOR II; COMPND 13 EC: 3.4.21.5; COMPND 14 ENGINEERED: YES; COMPND 15 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: F2; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_CELL: KIDNEY; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: HPC4-PNUT; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: F2; SOURCE 17 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 18 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 20 EXPRESSION_SYSTEM_CELL: KIDNEY; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: HPC4-PNUT KEYWDS THROMBIN, ANTICOAGULANT, BLOOD CLOTTING, PPACK, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.O.PINEDA,Z.-W.CHEN,S.CACCIA,S.N.SAVVIDES,G.WAKSMAN,F.S.MATHEWS,E.DI AUTHOR 2 CERA REVDAT 8 13-MAR-24 1TQ7 1 COMPND SOURCE REVDAT 7 23-AUG-23 1TQ7 1 REMARK REVDAT 6 27-OCT-21 1TQ7 1 SEQADV HETSYN REVDAT 5 29-JUL-20 1TQ7 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 13-JUL-11 1TQ7 1 VERSN REVDAT 3 24-FEB-09 1TQ7 1 VERSN REVDAT 2 12-OCT-04 1TQ7 1 JRNL AUTHOR REVDAT 1 03-AUG-04 1TQ7 0 JRNL AUTH A.O.PINEDA,Z.-W.CHEN,S.CACCIA,A.M.CANTWELL,S.N.SAVVIDES, JRNL AUTH 2 G.WAKSMAN,F.S.MATHEWS,E.DI CERA JRNL TITL THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A HAS A JRNL TITL 2 COLLAPSED PRIMARY SPECIFICITY POCKET JRNL REF J.BIOL.CHEM. V. 279 39824 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15252033 JRNL DOI 10.1074/JBC.M407272200 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 756394.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 12594 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 SET) : 0.205 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1299 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1767 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 195 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2379 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.80000 REMARK 3 B22 (A**2) : -8.63000 REMARK 3 B33 (A**2) : 7.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.680 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.570 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.110 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 28.62 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP-DAMINO.PARAM REMARK 3 PARAMETER FILE 2 : NAG.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CH2.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN-DAMINO.TOP REMARK 3 TOPOLOGY FILE 2 : NAG.TOPO REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CH2.TOPO REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TQ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 148 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13234 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 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: CNS REMARK 200 STARTING MODEL: 1PPB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.2 M ZINC ACETATE, 0.1 REMARK 280 M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.55500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.66500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.66500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.55500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.91500 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: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 KCAL/MOL 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 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 TRP B 147A REMARK 465 THR B 147B REMARK 465 ALA B 147C REMARK 465 ASN B 147D REMARK 465 VAL B 147E REMARK 465 GLY B 147F 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 GLN A 1O CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 1A ZN ZN A 402 1.37 REMARK 500 O LYS B 110 O HOH B 705 1.93 REMARK 500 O GLY A 1D N ALA A 1B 2.01 REMARK 500 O HOH A 505 O HOH A 758 2.02 REMARK 500 O HOH B 709 O HOH B 803 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 544 O HOH B 757 3655 0.43 REMARK 500 OE2 GLU B 127 ZN ZN A 402 4565 1.49 REMARK 500 NH1 ARG A 1I O HOH A 793 4465 2.03 REMARK 500 OE1 GLU B 97A O HOH B 805 3645 2.06 REMARK 500 OD2 ASP A 1A OE2 GLU B 127 4465 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 1K CG ASN A 1K ND2 0.233 REMARK 500 ASN A 1K C PRO A 1J N -0.172 REMARK 500 PRO A 1J CA PRO A 1J CB -0.282 REMARK 500 PRO A 1J CA PRO A 1J C -0.195 REMARK 500 PRO A 1J C PRO A 1J O 0.242 REMARK 500 PRO A 1J C ARG A 1I N 0.198 REMARK 500 ARG A 1I N ARG A 1I CA 0.130 REMARK 500 ARG A 1I CD ARG A 1I NE 0.316 REMARK 500 ARG A 1I NE ARG A 1I CZ 0.322 REMARK 500 ARG A 1I CZ ARG A 1I NH1 0.204 REMARK 500 ARG A 1I CZ ARG A 1I NH2 0.158 REMARK 500 ARG A 1I C ARG A 1I O -0.216 REMARK 500 THR A 1H N THR A 1H CA -0.207 REMARK 500 THR A 1H CB THR A 1H CG2 -0.297 REMARK 500 THR A 1H C THR A 1H O 0.134 REMARK 500 PHE A 1G N PHE A 1G CA -0.308 REMARK 500 PHE A 1G CA PHE A 1G CB -0.329 REMARK 500 PHE A 1G CB PHE A 1G CG 0.591 REMARK 500 PHE A 1G C PHE A 1G O -0.157 REMARK 500 GLY A 1F N GLY A 1F CA 0.302 REMARK 500 GLY A 1F CA GLY A 1F C -0.132 REMARK 500 SER A 1E CA SER A 1E CB 0.266 REMARK 500 SER A 1E CB SER A 1E OG 0.130 REMARK 500 SER A 1E C SER A 1E O -0.119 REMARK 500 GLY A 1D CA GLY A 1D C -0.132 REMARK 500 GLY A 1D C GLY A 1D O 0.109 REMARK 500 GLU A 1C N GLU A 1C CA 0.190 REMARK 500 GLU A 1C CA GLU A 1C CB -0.284 REMARK 500 GLU A 1C CG GLU A 1C CD -0.134 REMARK 500 GLU A 1C CD GLU A 1C OE1 0.269 REMARK 500 ALA A 1B C ALA A 1B O 0.156 REMARK 500 ASP A 1A CB ASP A 1A CG -0.297 REMARK 500 ASP A 1A CG ASP A 1A OD2 0.183 REMARK 500 ASP A 1A C CYS A 1 N -0.228 REMARK 500 CYS A 1 N CYS A 1 CA 0.144 REMARK 500 CYS A 1 C CYS A 1 O -0.163 REMARK 500 CYS A 1 C GLY A 2 N 0.170 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 1N N - CA - C ANGL. DEV. = 18.3 DEGREES REMARK 500 PHE A 1L O - C - N ANGL. DEV. = 14.9 DEGREES REMARK 500 ASN A 1K CB - CG - OD1 ANGL. DEV. = 16.3 DEGREES REMARK 500 PRO A 1J C - N - CA ANGL. DEV. = 17.3 DEGREES REMARK 500 PRO A 1J CB - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 PRO A 1J N - CA - CB ANGL. DEV. = 19.1 DEGREES REMARK 500 PRO A 1J N - CA - C ANGL. DEV. = -22.6 DEGREES REMARK 500 PRO A 1J O - C - N ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG A 1I CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 ARG A 1I N - CA - CB ANGL. DEV. = -14.3 DEGREES REMARK 500 ARG A 1I CD - NE - CZ ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 1I NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 1I NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 THR A 1H N - CA - CB ANGL. DEV. = 15.3 DEGREES REMARK 500 THR A 1H CA - CB - OG1 ANGL. DEV. = -21.5 DEGREES REMARK 500 PHE A 1G CD1 - CG - CD2 ANGL. DEV. = 11.4 DEGREES REMARK 500 PHE A 1G CB - CG - CD1 ANGL. DEV. = -9.9 DEGREES REMARK 500 PHE A 1G CG - CD1 - CE1 ANGL. DEV. = -7.8 DEGREES REMARK 500 PHE A 1G CA - C - O ANGL. DEV. = 21.6 DEGREES REMARK 500 PHE A 1G CA - C - N ANGL. DEV. = -14.8 DEGREES REMARK 500 SER A 1E N - CA - CB ANGL. DEV. = -16.6 DEGREES REMARK 500 SER A 1E N - CA - C ANGL. DEV. = 29.9 DEGREES REMARK 500 SER A 1E CA - C - O ANGL. DEV. = -28.5 DEGREES REMARK 500 SER A 1E O - C - N ANGL. DEV. = 24.9 DEGREES REMARK 500 ALA A 1B CA - C - O ANGL. DEV. = -14.0 DEGREES REMARK 500 ASP A 1A OD1 - CG - OD2 ANGL. DEV. = -14.1 DEGREES REMARK 500 ASP A 1A CB - CG - OD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 CYS A 1 CA - CB - SG ANGL. DEV. = 10.1 DEGREES REMARK 500 GLY A 2 C - N - CA ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG B 77A N - CA - C ANGL. DEV. = 20.1 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 GLN A 1O 138.31 75.67 REMARK 500 GLU A 1C -16.67 -40.85 REMARK 500 ASP A 1A 43.37 -108.12 REMARK 500 PHE A 7 -85.03 -133.71 REMARK 500 ASP A 14L -159.68 -37.29 REMARK 500 TYR B 60A 81.61 -161.45 REMARK 500 ASN B 60G 55.25 -156.23 REMARK 500 GLU B 77 79.00 -104.76 REMARK 500 ARG B 77A -95.71 27.92 REMARK 500 ILE B 79 -74.06 -106.21 REMARK 500 GLU B 97A -82.37 -112.60 REMARK 500 PRO B 111 152.47 -47.35 REMARK 500 ARG B 175 97.98 -64.42 REMARK 500 SER B 214 -56.88 -123.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 1F SER A 1E 144.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PRO A 1J 11.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE REMARK 600 RESIDUES: REMARK 600 1) VIA A HEMIKETAL GROUP TO OG SER B 195, REMARK 600 2) VIA A METHYLENE GROUP TO NE2 HIS B 57. 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 14E OE1 REMARK 620 2 HOH B 503 O 99.5 REMARK 620 N 1 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0G6 B 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL DBREF 1TQ7 A 1 15 UNP P00734 THRB_HUMAN 320 363 DBREF 1TQ7 B 16 245 UNP P00734 THRB_HUMAN 364 620 SEQADV 1TQ7 ALA B 215 UNP P00734 TRP 590 ENGINEERED MUTATION SEQADV 1TQ7 ALA B 217 UNP P00734 GLU 592 ENGINEERED MUTATION SEQRES 1 A 44 TYR GLN THR PHE PHE ASN PRO ARG THR PHE GLY SER GLY SEQRES 2 A 44 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 3 A 44 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 4 A 44 TYR ILE ASP GLY ARG SEQRES 1 B 257 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 257 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 257 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 257 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 257 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 257 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 257 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 257 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 257 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 257 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 257 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 257 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 257 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 257 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 257 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 257 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 257 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 257 MET GLY ILE VAL SER ALA GLY ALA GLY CYS ASP ARG ASP SEQRES 19 B 257 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 257 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE MODRES 1TQ7 ASN B 60G ASN GLYCOSYLATION SITE HET ZN A 401 1 HET ZN A 402 1 HET 0G6 B 301 30 HET NAG B 600 14 HET ZN B 403 1 HETNAM ZN ZINC ION HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN 0G6 PPACK HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 ZN 3(ZN 2+) FORMUL 5 0G6 C21 H34 CL N6 O3 1+ FORMUL 6 NAG C8 H15 N O6 FORMUL 8 HOH *145(H2 O) HELIX 1 1 ASN A 1K GLY A 1F 1 6 HELIX 2 2 PHE A 7 SER A 11 5 5 HELIX 3 3 THR A 14B TYR A 14J 1 9 HELIX 4 4 ALA B 55 LEU B 59 1 5 HELIX 5 5 PRO B 60B ASP B 60E 5 4 HELIX 6 6 THR B 60I ASN B 62 5 3 HELIX 7 7 ASP B 125 LEU B 130 1 9 HELIX 8 8 GLU B 164 THR B 172 1 9 HELIX 9 9 LYS B 185 GLY B 186C 5 5 HELIX 10 10 LEU B 234 GLN B 244 1 11 SHEET 1 A 7 SER B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N GLY B 136 O LEU B 160 SHEET 4 A 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 A 7 TRP B 207 ALA B 215 -1 O TYR B 208 N MET B 201 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O PHE B 227 N ALA B 215 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 GLN B 30 ARG B 35 0 SHEET 2 B 7 GLU B 39 LEU B 46 -1 O LEU B 41 N LEU B 33 SHEET 3 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 B 7 ALA B 104 LEU B 108 -1 O MET B 106 N VAL B 52 SHEET 5 B 7 LYS B 81 ILE B 90 -1 N GLU B 86 O LYS B 107 SHEET 6 B 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 7 B 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 1 C 2 LEU B 60 TYR B 60A 0 SHEET 2 C 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 1.81 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.03 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.03 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.02 LINK NE2 HIS B 57 C3 0G6 B 301 1555 1555 1.64 LINK ND2 ASN B 60G C1 NAG B 600 1555 1555 1.63 LINK OG SER B 195 C2 0G6 B 301 1555 1555 1.81 LINK OE1 GLU A 14E ZN ZN A 401 1555 1555 2.23 LINK ZN ZN A 401 O HOH B 503 1555 1555 2.35 LINK ZN ZN A 402 NE2 HIS B 119 1555 1555 2.25 LINK ND1 HIS B 71 ZN ZN B 403 1555 1555 2.28 CISPEP 1 SER B 36A PRO B 37 0 -0.60 CRYST1 51.110 73.830 87.330 90.00 90.00 90.00 P 21 21 21 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 0.019566 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011451 0.00000