PDB Short entry for 1HAP HEADER HYDROLASE/HYDROLASE INHIBITOR/DNA 03-OCT-95 1HAP TITLE COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE TITLE 2 GGTTGGTGTGGTTGG (BASED ON X-RAY MODEL OF DNA) CAVEAT 1HAP THE BONDS OG SER H 195-C2 0G6 AND NE2 HIS H 57-C3 0G6 ARE CAVEAT 2 1HAP OUTSIDE ACCEPTED RANGE CAVEAT 1HAP THE INTERACTIONS INVOLVING DT 407, DG 408, AND DT 413 ARE CAVEAT 2 1HAP OUTSIDE ACCEPTED RANGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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: THROMBIN LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 FRAGMENT: RESIDUES 328-363; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 13 CHAIN: H; COMPND 14 FRAGMENT: RESIDUES 364-622; COMPND 15 SYNONYM: COAGULATION FACTOR II; 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 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606 KEYWDS COAGULATION, QUADRUPLE HELIX, HYDROLASE-HYDROLASE INHIBITOR-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.PADMANABHAN,A.TULINSKY REVDAT 3 13-JUL-11 1HAP 1 VERSN REVDAT 2 24-FEB-09 1HAP 1 VERSN REVDAT 1 03-APR-96 1HAP 0 JRNL AUTH K.PADMANABHAN,A.TULINSKY JRNL TITL AN AMBIGUOUS STRUCTURE OF A DNA 15-MER THROMBIN COMPLEX. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 52 272 1996 JRNL REFN ISSN 0907-4449 JRNL PMID 15299700 JRNL DOI 10.1107/S0907444995013977 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.PADMANABHAN,K.P.PADMANABHAN,J.D.FERRARA,J.E.SADLER, REMARK 1 AUTH 2 A.TULINSKY REMARK 1 TITL THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER REMARK 1 TITL 2 SINGLE-STRANDED DNA APTAMER REMARK 1 REF J.BIOL.CHEM. V. 268 17651 1993 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLIN, PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 68.0 REMARK 3 NUMBER OF REFLECTIONS : 7717 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 + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2275 REMARK 3 NUCLEIC ACID ATOMS : 315 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 151 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 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 : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9225 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 57.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 (%): 57.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 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 29.14000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.01000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.80500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.01000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.14000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.80500 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 L -5 REMARK 465 PHE L -4 REMARK 465 GLY L -3 REMARK 465 SER L -2 REMARK 465 GLY L -1 REMARK 465 GLU L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 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 C7 DT D 407 CG2 ILE H 24 0.93 REMARK 500 O4' DG D 408 NH2 ARG H 75 1.24 REMARK 500 C4' DG D 408 NH2 ARG H 75 1.49 REMARK 500 C2' DG D 408 NH2 ARG H 75 1.62 REMARK 500 C1' DG D 408 NH2 ARG H 75 1.66 REMARK 500 C8 DG D 408 NE ARG H 75 1.71 REMARK 500 C7 DT D 407 CB ILE H 24 1.74 REMARK 500 OG SER H 195 O2 0G6 H 297 1.89 REMARK 500 OE2 GLU L 8 NZ LYS H 202 1.90 REMARK 500 C5 DT D 407 CG2 ILE H 24 1.92 REMARK 500 C3' DG D 408 NH2 ARG H 75 1.95 REMARK 500 N2 DG D 402 N7 DG D 405 1.96 REMARK 500 C2' DT D 413 OP2 DG D 414 1.96 REMARK 500 C5' DG D 408 NH1 ARG H 75 1.97 REMARK 500 C5' DG D 408 NH2 ARG H 75 2.01 REMARK 500 O6 DG D 402 N1 DG D 414 2.04 REMARK 500 CB SER H 195 O2 0G6 H 297 2.04 REMARK 500 OD2 ASP H 49 OE2 GLU H 247 2.05 REMARK 500 NE1 TRP H 51 N GLU H 247 2.05 REMARK 500 O5' DT D 407 O4 DT D 409 2.05 REMARK 500 O MET H 84 N LYS H 109 2.07 REMARK 500 O4' DT D 407 N3 DT D 409 2.09 REMARK 500 O4' DG D 408 CZ ARG H 75 2.10 REMARK 500 OG1 THR H 172 N ILE H 174 2.15 REMARK 500 N CYS H 191 OD2 ASP H 194 2.18 REMARK 500 N HIS H 71 OE2 GLU H 77 2.18 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 OP2 DT D 413 NH1 ARG H 101 2564 1.15 REMARK 500 P DT D 413 NH1 ARG H 101 2564 1.50 REMARK 500 C5' DT D 413 NE ARG H 101 2564 1.58 REMARK 500 O5' DT D 413 NH1 ARG H 101 2564 1.72 REMARK 500 C5' DT D 413 CZ ARG H 101 2564 1.80 REMARK 500 C5' DT D 413 CD ARG H 101 2564 1.84 REMARK 500 O5' DT D 413 CZ ARG H 101 2564 2.08 REMARK 500 C5' DT D 413 NH1 ARG H 101 2564 2.15 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' 0.071 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 O5' - C5' - C4' ANGL. DEV. = 17.3 DEGREES REMARK 500 DG D 401 O4' - C4' - C3' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG D 402 O5' - C5' - C4' ANGL. DEV. = -9.8 DEGREES REMARK 500 DG D 402 P - O5' - C5' ANGL. DEV. = -11.2 DEGREES REMARK 500 DG D 402 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG D 402 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT D 403 P - O5' - C5' ANGL. DEV. = 9.6 DEGREES REMARK 500 DT D 403 C4' - C3' - O3' ANGL. DEV. = 13.5 DEGREES REMARK 500 DT D 403 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DT D 403 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT D 403 C2 - N3 - C4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT D 403 N3 - C4 - C5 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT D 404 C5' - C4' - C3' ANGL. DEV. = 16.2 DEGREES REMARK 500 DT D 404 C5' - C4' - O4' ANGL. DEV. = -17.1 DEGREES REMARK 500 DT D 404 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DT D 404 C4' - C3' - O3' ANGL. DEV. = 13.2 DEGREES REMARK 500 DT D 404 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT D 404 C2 - N3 - C4 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT D 404 N3 - C4 - C5 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT D 404 N3 - C2 - O2 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT D 404 N3 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT D 403 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DT D 404 O3' - P - O5' ANGL. DEV. = 16.2 DEGREES REMARK 500 DG D 405 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG D 405 C3' - C2' - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 DT D 404 C3' - O3' - P ANGL. DEV. = 32.1 DEGREES REMARK 500 DG D 405 O3' - P - OP2 ANGL. DEV. = 7.3 DEGREES REMARK 500 DG D 406 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 DG D 406 C3' - C2' - C1' ANGL. DEV. = -8.8 DEGREES REMARK 500 DG D 406 O4' - C1' - N9 ANGL. DEV. = 11.7 DEGREES REMARK 500 DG D 406 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG D 405 C3' - O3' - P ANGL. DEV. = 23.0 DEGREES REMARK 500 DT D 407 C3' - C2' - C1' ANGL. DEV. = -6.6 DEGREES REMARK 500 DT D 407 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DT D 407 C2 - N3 - C4 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT D 407 N3 - C4 - C5 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG D 408 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG D 408 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DT D 409 OP1 - P - OP2 ANGL. DEV. = -12.3 DEGREES REMARK 500 DT D 409 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT D 409 N1 - C2 - N3 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT D 409 C2 - N3 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT D 409 N3 - C4 - O4 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG D 408 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 DG D 410 O5' - C5' - C4' ANGL. DEV. = -9.4 DEGREES REMARK 500 DT D 409 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DG D 411 O5' - P - OP1 ANGL. DEV. = 7.9 DEGREES REMARK 500 DG D 411 O5' - C5' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG D 411 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 DG D 411 C3' - C2' - C1' ANGL. DEV. = -9.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 132 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 ASP L 1A 62.21 -104.07 REMARK 500 PHE L 7 -75.02 -122.38 REMARK 500 TYR L 14J -9.08 -49.63 REMARK 500 SER H 27 78.97 -158.27 REMARK 500 LYS H 36 -70.74 -78.43 REMARK 500 GLN H 38 91.17 -61.17 REMARK 500 SER H 48 155.74 177.48 REMARK 500 ASP H 49 -15.11 -39.91 REMARK 500 ARG H 50 -34.60 -134.79 REMARK 500 HIS H 57 -3.77 -54.53 REMARK 500 ASP H 60E 17.88 86.13 REMARK 500 ASN H 60G 75.06 -157.25 REMARK 500 GLU H 61 -32.20 -29.36 REMARK 500 HIS H 71 -74.99 -153.24 REMARK 500 GLU H 77 85.68 -58.61 REMARK 500 ARG H 77A -42.84 -29.50 REMARK 500 ILE H 79 -50.35 -120.90 REMARK 500 ARG H 93 22.36 -79.23 REMARK 500 GLU H 97A -61.77 -90.62 REMARK 500 ASN H 98 11.06 -159.20 REMARK 500 ARG H 101 60.36 39.85 REMARK 500 LYS H 109 -71.73 -63.15 REMARK 500 LEU H 130 92.30 -67.55 REMARK 500 TRP H 141 47.85 -81.27 REMARK 500 ARG H 165 -51.07 -26.18 REMARK 500 GLU H 186B -2.81 -49.43 REMARK 500 LYS H 186D 143.94 -172.42 REMARK 500 ASP H 189 164.07 178.39 REMARK 500 GLU H 192 103.58 -52.11 REMARK 500 SER H 195 135.50 -29.62 REMARK 500 PRO H 204 34.81 -97.66 REMARK 500 ASN H 204B -6.51 -141.96 REMARK 500 SER H 214 -56.11 -124.73 REMARK 500 TRP H 215 -156.89 -163.18 REMARK 500 ASP H 221 52.05 71.22 REMARK 500 HIS H 230 83.27 -67.12 REMARK 500 PHE H 232 -76.94 -33.90 REMARK 500 ARG H 233 -29.86 -27.72 REMARK 500 ASP H 243 37.02 -92.94 REMARK 500 GLN H 244 -32.32 -149.12 REMARK 500 PHE H 245 25.80 -170.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG D 401 0.06 SIDE CHAIN REMARK 500 ARG L 14D 0.12 SIDE CHAIN 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 PHE H 60H 13.06 REMARK 500 ASN H 78 -12.65 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 LEU H 33 45.4 L L OUTSIDE RANGE REMARK 500 ALA H 55 46.1 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 663 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH D 672 DISTANCE = 7.70 ANGSTROMS REMARK 525 HOH D 679 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH D 681 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH D 698 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH H 531 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH H 560 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH H 587 DISTANCE = 5.40 ANGSTROMS REMARK 525 HOH H 590 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH H 633 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH H 641 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH H 647 DISTANCE = 5.08 ANGSTROMS REMARK 525 HOH H 651 DISTANCE = 5.47 ANGSTROMS REMARK 525 HOH H 652 DISTANCE = 7.79 ANGSTROMS REMARK 525 HOH H 661 DISTANCE = 5.03 ANGSTROMS REMARK 525 HOH H 662 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH H 664 DISTANCE = 7.65 ANGSTROMS REMARK 525 HOH H 665 DISTANCE = 7.61 ANGSTROMS REMARK 525 HOH H 667 DISTANCE = 5.27 ANGSTROMS REMARK 525 HOH H 669 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH H 671 DISTANCE = 7.93 ANGSTROMS REMARK 525 HOH H 674 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH H 675 DISTANCE = 5.20 ANGSTROMS REMARK 525 HOH H 676 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH H 677 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH H 678 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH H 684 DISTANCE = 8.02 ANGSTROMS REMARK 525 HOH H 694 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH H 697 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH H 699 DISTANCE = 5.56 ANGSTROMS REMARK 525 HOH H 700 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH L 660 DISTANCE = 7.14 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE REMARK 600 UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. REMARK 600 UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A REMARK 600 COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT REMARK 600 BOND TO NE2 OF HIS 57 REMARK 630 REMARK 630 MOLECULE TYPE: NULL 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 H 297 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 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 0G6 H 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HAO RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHYMOTRYPSIN NUMBERING SYSTEM IS USED FOR THROMBIN, BASED REMARK 999 ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF REMARK 999 CHYMOTRYPSIN (BODE, W., ET AL., 1989, EMBO J. 8, 3467 - REMARK 999 3475). DBREF 1HAP L 1B 14K UNP P00734 THRB_HUMAN 328 363 DBREF 1HAP H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1HAP D 401 415 PDB 1HAP 1HAP 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 0G6 H 297 30 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 HETSYN 0G6 PPACK FORMUL 4 0G6 C21 H34 CL N6 O3 1+ FORMUL 5 HOH *151(H2 O) HELIX 1 1 GLU L 14C LEU L 14G 1 5 HELIX 2 2 PRO H 60B TRP H 60D 5 3 HELIX 3 3 ARG H 126 LEU H 129C 1 7 HELIX 4 4 ARG H 165 ASP H 170 1 6 HELIX 5 5 PHE H 232 PHE H 245 5 14 SHEET 1 A 4 LYS H 81 SER H 83 0 SHEET 2 A 4 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 A 4 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 A 4 GLU H 39 SER H 45 -1 N ALA H 44 O VAL H 31 SHEET 1 B 3 TRP H 51 THR H 54 0 SHEET 2 B 3 ALA H 104 LEU H 108 -1 N MET H 106 O VAL H 52 SHEET 3 B 3 LEU H 85 ILE H 90 -1 N TYR H 89 O LEU H 105 SHEET 1 C 2 LYS H 135 THR H 139 0 SHEET 2 C 2 VAL H 157 PRO H 161 -1 N LEU H 160 O GLY H 136 SHEET 1 D 2 MET H 180 ALA H 183 0 SHEET 2 D 2 GLY H 226 THR H 229 -1 N TYR H 228 O PHE H 181 SHEET 1 E 2 PRO H 198 SER H 203 0 SHEET 2 E 2 ARG H 206 ILE H 212 -1 N GLY H 211 O PHE H 199 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.01 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.09 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.00 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK OG SER H 195 C2 0G6 H 297 1555 1555 1.85 LINK NE2 HIS H 57 C3 0G6 H 297 1555 1555 1.94 CISPEP 1 SER H 36A PRO H 37 0 -2.34 SITE 1 AC1 13 HIS H 57 TYR H 60A TRP H 60D LEU H 99 SITE 2 AC1 13 ASP H 189 ALA H 190 ASP H 194 SER H 195 SITE 3 AC1 13 SER H 214 TRP H 215 GLY H 216 GLY H 219 SITE 4 AC1 13 GLY H 226 SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195 CRYST1 58.280 77.610 100.020 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 0.017159 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009998 0.00000