HEADER HYDROLASE/HYDROLASE INHIBITOR/DNA 27-MAY-93 1HUT TITLE THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED TITLE 2 DNA APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ALPHA-THROMBIN LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 FRAGMENT: RESIDUES 328-363; COMPND 9 SYNONYM: COAGULATION FACTOR II, THROMBIN; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ALPHA-THROMBIN HEAVY CHAIN; COMPND 13 CHAIN: H; COMPND 14 FRAGMENT: RESIDUES 364-622; COMPND 15 SYNONYM: COAGULATION FACTOR II, THROMBIN; COMPND 16 EC: 3.4.21.5 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 TISSUE: BLOOD; SOURCE 8 SECRETION: PLASMA; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 TISSUE: BLOOD; SOURCE 14 SECRETION: PLASMA KEYWDS THROMBIN, BLOOD CLOTTING, HYDROLASE-HYDROLASE INHIBITOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.PADMANABHAN,K.P.PADMANABHAN,J.D.FERRARA,J.E.SADLER,A.TULINSKY REVDAT 4 27-JUL-11 1HUT 1 HETATM HETNAM HETSYN REMARK REVDAT 3 13-JUL-11 1HUT 1 VERSN REVDAT 2 24-FEB-09 1HUT 1 VERSN REVDAT 1 22-JUN-94 1HUT 0 JRNL AUTH K.PADMANABHAN,K.P.PADMANABHAN,J.D.FERRARA,J.E.SADLER, JRNL AUTH 2 A.TULINSKY JRNL TITL THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER JRNL TITL 2 SINGLE-STRANDED DNA APTAMER. JRNL REF J.BIOL.CHEM. V. 268 17651 1993 JRNL REFN ISSN 0021-9258 JRNL PMID 8102368 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6806 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2340 REMARK 3 NUCLEIC ACID ATOMS : 315 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 3.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HUT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6990 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 28.26000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.76000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.76000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.26000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.72000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, L, H 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 THR H 148A REMARK 465 ALA H 148B REMARK 465 ASN H 148C REMARK 465 VAL H 148D REMARK 465 GLY H 148E REMARK 465 LYS H 148F 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 O TYR L 14J N ASP L 14L 1.92 REMARK 500 NZ LYS H 36 O ASN H 62 1.93 REMARK 500 O GLU H 127 OG SER H 129B 2.02 REMARK 500 O4' DT D 407 N3 DT D 409 2.07 REMARK 500 NE2 GLN H 30 O THR H 139 2.07 REMARK 500 O6 DG D 402 N1 DG D 414 2.12 REMARK 500 O THR H 60I CB ASP H 63 2.16 REMARK 500 CB CYS H 42 O SER H 195 2.16 REMARK 500 N7 DG D 406 N2 DG D 410 2.17 REMARK 500 N2 DG D 402 N7 DG D 405 2.19 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 DG D 401 O4' DG D 401 C1' 0.081 REMARK 500 DG D 402 O4' DG D 402 C1' 0.075 REMARK 500 DT D 404 O4' DT D 404 C4' 0.074 REMARK 500 DG D 405 P DG D 405 O5' 0.063 REMARK 500 DT D 407 C3' DT D 407 C2' 0.110 REMARK 500 DG D 408 O4' DG D 408 C1' 0.078 REMARK 500 DT D 413 O4' DT D 413 C1' 0.079 REMARK 500 GLY L 1F C SER L 1E N 0.173 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 DG D 401 C5' - C4' - O4' ANGL. DEV. = 12.3 DEGREES REMARK 500 DG D 402 O5' - C5' - C4' ANGL. DEV. = -11.1 DEGREES REMARK 500 DG D 402 P - O5' - C5' ANGL. DEV. = -11.4 DEGREES REMARK 500 DG D 402 O4' - C4' - C3' ANGL. DEV. = -4.6 DEGREES REMARK 500 DG D 402 C1' - O4' - C4' ANGL. DEV. = -11.6 DEGREES REMARK 500 DG D 402 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT D 403 OP1 - P - OP2 ANGL. DEV. = -25.5 DEGREES REMARK 500 DT D 403 O5' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 DT D 403 C4' - C3' - O3' ANGL. DEV. = 17.2 DEGREES REMARK 500 DT D 403 O4' - C1' - N1 ANGL. DEV. = 10.7 DEGREES REMARK 500 DT D 403 C6 - N1 - C2 ANGL. DEV. = -3.3 DEGREES REMARK 500 DT D 403 N1 - C2 - N3 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT D 403 C2 - N3 - C4 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT D 403 N3 - C4 - C5 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG D 402 C3' - O3' - P ANGL. DEV. = 23.8 DEGREES REMARK 500 DT D 404 O5' - P - OP1 ANGL. DEV. = 12.9 DEGREES REMARK 500 DT D 404 O5' - P - OP2 ANGL. DEV. = -7.5 DEGREES REMARK 500 DT D 404 P - O5' - C5' ANGL. DEV. = 21.1 DEGREES REMARK 500 DT D 404 O4' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 DT D 404 C5' - C4' - C3' ANGL. DEV. = 16.6 DEGREES REMARK 500 DT D 404 C1' - O4' - C4' ANGL. DEV. = -14.6 DEGREES REMARK 500 DT D 404 C4' - C3' - O3' ANGL. DEV. = 17.3 DEGREES REMARK 500 DT D 404 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 DT D 404 O4' - C1' - N1 ANGL. DEV. = 15.7 DEGREES REMARK 500 DT D 404 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT D 404 N1 - C2 - N3 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT D 404 C2 - N3 - C4 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT D 404 N3 - C4 - C5 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT D 404 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT D 403 C3' - O3' - P ANGL. DEV. = -7.7 DEGREES REMARK 500 DT D 404 O3' - P - O5' ANGL. DEV. = 19.0 DEGREES REMARK 500 DG D 405 O5' - P - OP1 ANGL. DEV. = -7.4 DEGREES REMARK 500 DG D 405 C5' - C4' - C3' ANGL. DEV. = 8.3 DEGREES REMARK 500 DG D 405 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 404 C3' - O3' - P ANGL. DEV. = 22.2 DEGREES REMARK 500 DG D 405 O3' - P - OP2 ANGL. DEV. = 8.2 DEGREES REMARK 500 DG D 406 OP1 - P - OP2 ANGL. DEV. = -13.1 DEGREES REMARK 500 DG D 406 P - O5' - C5' ANGL. DEV. = 17.4 DEGREES REMARK 500 DG D 406 N9 - C1' - C2' ANGL. DEV. = -12.1 DEGREES REMARK 500 DG D 406 O4' - C1' - N9 ANGL. DEV. = 23.3 DEGREES REMARK 500 DG D 406 N1 - C6 - O6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG D 405 C3' - O3' - P ANGL. DEV. = 23.0 DEGREES REMARK 500 DT D 407 O5' - P - OP1 ANGL. DEV. = 9.0 DEGREES REMARK 500 DT D 407 O5' - C5' - C4' ANGL. DEV. = -7.7 DEGREES REMARK 500 DT D 407 C5' - C4' - C3' ANGL. DEV. = 8.8 DEGREES REMARK 500 DT D 407 C1' - O4' - C4' ANGL. DEV. = -10.0 DEGREES REMARK 500 DT D 407 C4' - C3' - O3' ANGL. DEV. = 14.6 DEGREES REMARK 500 DT D 407 C4' - C3' - C2' ANGL. DEV. = -10.2 DEGREES REMARK 500 DT D 407 C3' - C2' - C1' ANGL. DEV. = -14.9 DEGREES REMARK 500 DT D 407 N1 - C1' - C2' ANGL. DEV. = -15.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 157 ANGLE DEVIATIONS. 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 PHE L 1G -158.66 -41.87 REMARK 500 SER L 1E 22.08 44.30 REMARK 500 ALA L 1B -39.33 178.61 REMARK 500 PHE L 7 -73.41 -125.73 REMARK 500 LYS L 9 -7.69 -47.61 REMARK 500 SER L 11 38.84 38.08 REMARK 500 LYS L 14A -65.61 -29.97 REMARK 500 ARG L 14D -7.81 -54.70 REMARK 500 LEU L 14G 2.97 -51.70 REMARK 500 TYR L 14J 90.08 -66.98 REMARK 500 ILE L 14K 87.75 -33.82 REMARK 500 ASP L 14L 98.53 70.14 REMARK 500 GLU H 18 68.73 36.64 REMARK 500 SER H 20 103.64 -171.73 REMARK 500 ASP H 21 111.78 -26.00 REMARK 500 ARG H 50 11.53 -169.01 REMARK 500 THR H 54 -168.71 -118.37 REMARK 500 LEU H 59 -10.37 -142.41 REMARK 500 ASN H 60G 83.48 -160.22 REMARK 500 GLU H 61 -69.69 -25.38 REMARK 500 HIS H 71 -53.10 -142.36 REMARK 500 ARG H 77A -56.25 -26.70 REMARK 500 ILE H 79 -64.17 -91.52 REMARK 500 ASN H 98 60.57 -160.13 REMARK 500 LEU H 99 46.03 36.57 REMARK 500 ALA H 104 137.11 -176.60 REMARK 500 PHE H 114 43.66 -108.82 REMARK 500 ASP H 116 9.88 25.22 REMARK 500 TYR H 117 -0.80 -164.59 REMARK 500 PRO H 124 162.19 -45.55 REMARK 500 GLU H 127 -70.85 -54.75 REMARK 500 LEU H 130 42.68 -69.21 REMARK 500 ASN H 143 146.07 -36.94 REMARK 500 PRO H 166 1.62 -60.95 REMARK 500 CYS H 168 8.50 -67.89 REMARK 500 LYS H 169 -68.64 -101.70 REMARK 500 ASP H 170 23.74 -76.65 REMARK 500 ILE H 174 153.33 -43.66 REMARK 500 ASP H 178 21.32 -72.60 REMARK 500 ASP H 186A 54.14 -94.69 REMARK 500 GLU H 186B 61.34 -160.11 REMARK 500 SER H 195 143.13 -31.38 REMARK 500 TRP H 215 -161.71 -168.08 REMARK 500 GLU H 217 66.00 -102.18 REMARK 500 CYS H 220 120.93 -29.61 REMARK 500 ASP H 222 99.27 -68.94 REMARK 500 HIS H 230 80.40 -56.52 REMARK 500 ARG H 233 9.63 -50.25 REMARK 500 LEU H 234 -1.30 -144.83 REMARK 500 ILE H 238 -79.41 -67.82 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 ILE L 14K 12.21 REMARK 500 LYS H 36 -13.01 REMARK 500 ASP H 63 13.49 REMARK 500 LEU H 64 10.76 REMARK 500 LYS H 81 10.54 REMARK 500 SER H 153 10.78 REMARK 500 VAL H 200 17.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 DG D 411 -48.9 D D OUTSIDE RANGE REMARK 500 THR H 229 24.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D 603 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH D 615 DISTANCE = 8.15 ANGSTROMS REMARK 525 HOH D 618 DISTANCE = 8.81 ANGSTROMS REMARK 525 HOH D 621 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH D 623 DISTANCE = 5.57 ANGSTROMS REMARK 525 HOH D 630 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH D 632 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH D 644 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH D 645 DISTANCE = 10.12 ANGSTROMS REMARK 525 HOH D 652 DISTANCE = 8.37 ANGSTROMS REMARK 525 HOH D 677 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH H 502 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH H 516 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH H 523 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH H 573 DISTANCE = 5.28 ANGSTROMS REMARK 525 HOH H 575 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH H 592 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH H 594 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH H 611 DISTANCE = 9.36 ANGSTROMS REMARK 525 HOH H 612 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH H 613 DISTANCE = 5.11 ANGSTROMS REMARK 525 HOH H 616 DISTANCE = 7.66 ANGSTROMS REMARK 525 HOH H 617 DISTANCE = 5.23 ANGSTROMS REMARK 525 HOH H 619 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH H 620 DISTANCE = 9.97 ANGSTROMS REMARK 525 HOH H 622 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH H 625 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH H 626 DISTANCE = 5.20 ANGSTROMS REMARK 525 HOH H 627 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH H 629 DISTANCE = 8.18 ANGSTROMS REMARK 525 HOH H 633 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH H 638 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH H 639 DISTANCE = 11.68 ANGSTROMS REMARK 525 HOH H 641 DISTANCE = 8.00 ANGSTROMS REMARK 525 HOH H 643 DISTANCE = 8.87 ANGSTROMS REMARK 525 HOH H 646 DISTANCE = 9.72 ANGSTROMS REMARK 525 HOH H 650 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH H 654 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH H 655 DISTANCE = 7.99 ANGSTROMS REMARK 525 HOH H 656 DISTANCE = 10.26 ANGSTROMS REMARK 525 HOH H 657 DISTANCE = 8.95 ANGSTROMS REMARK 525 HOH H 658 DISTANCE = 8.03 ANGSTROMS REMARK 525 HOH H 662 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH H 664 DISTANCE = 8.72 ANGSTROMS REMARK 525 HOH H 665 DISTANCE = 5.36 ANGSTROMS REMARK 525 HOH H 667 DISTANCE = 8.48 ANGSTROMS REMARK 525 HOH H 669 DISTANCE = 5.66 ANGSTROMS REMARK 525 HOH H 670 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH H 672 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH H 673 DISTANCE = 9.29 ANGSTROMS REMARK 525 HOH H 674 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH H 679 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH H 680 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH H 685 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH L 640 DISTANCE = 5.65 ANGSTROMS REMARK 525 HOH L 666 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH L 671 DISTANCE = 8.02 ANGSTROMS REMARK 525 HOH L 678 DISTANCE = 6.21 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 0G7 H 1 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO- REMARK 630 2-OXOHEXAN-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 0G7 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO ARG 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0G7 H 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHYMOTRYPSIN NUMBERING SYSTEM IS USED BASED ON THE TOPOLOGICAL REMARK 999 ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, REMARK 999 EMBO J. 8, 3467-3475). THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND REMARK 999 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN REMARK 999 INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN CHAIN INDICATOR REMARK 999 *D* IS USED FOR THE OLIGONUCLEOTIDE. DBREF 1HUT L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1HUT H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1HUT D 401 415 PDB 1HUT 1HUT 401 415 SEQRES 1 D 15 DG DG DT DT DG DG DT DG DT DG DG DT DT SEQRES 2 D 15 DG DG SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU HET 0G7 H 1 30 HETNAM 0G7 D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2- HETNAM 2 0G7 OXOHEXAN-3-YL]-L-PROLINAMIDE HETSYN 0G7 D-PHE-PRO-ARG CHLOROMETHYLKETONE (PPACK) FORMUL 4 0G7 C21 H31 CL N6 O3 FORMUL 5 HOH *130(H2 O) HELIX 1 4 ASP H 125 LEU H 130 1 9 HELIX 2 5 GLU H 164 LYS H 169 1 6 HELIX 3 6 LEU H 234 PHE H 245 1 12 SHEET 1 A 4 GLU H 39 LEU H 40 0 SHEET 2 A 4 LEU H 33 ARG H 35 -1 N ARG H 35 O GLU H 39 SHEET 3 A 4 LEU H 64 ILE H 68 -1 N LEU H 65 O PHE H 34 SHEET 4 A 4 LYS H 81 SER H 83 -1 O LYS H 81 N ILE H 68 SHEET 1 B 4 SER H 45 LEU H 46 0 SHEET 2 B 4 TRP H 51 THR H 54 -1 N LEU H 53 O SER H 45 SHEET 3 B 4 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 4 B 4 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 1 C 2 LEU H 60 TYR H 60A 0 SHEET 2 C 2 LYS H 60F ASN H 60G-1 N LYS H 60F O TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.03 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.02 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.00 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.02 CISPEP 1 SER H 36A PRO H 37 0 -4.89 SITE 1 AC1 14 HIS H 57 TYR H 60A TRP H 60D ASN H 98 SITE 2 AC1 14 LEU H 99 ILE H 174 ASP H 189 ALA H 190 SITE 3 AC1 14 CYS H 191 SER H 195 SER H 214 TRP H 215 SITE 4 AC1 14 GLY H 216 CYS H 220 SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195 CRYST1 56.520 77.440 99.520 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 0.017693 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010048 0.00000