PDB Short entry for 1YCP HEADER HYDROLASE/HYDROLASE SUBSTRATE 01-MAY-97 1YCP TITLE THE CRYSTAL STRUCTURE OF FIBRINOGEN-AA PEPTIDE 1-23 (F8Y) BOUND TO TITLE 2 BOVINE THROMBIN EXPLAINS WHY THE MUTATION OF PHE-8 TO TYROSINE TITLE 3 STRONGLY INHIBITS NORMAL CLEAVAGE AT ARGININE-16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPSILON THROMBIN; COMPND 3 CHAIN: L, J; COMPND 4 EC: 3.4.21.5; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ALPHA THROMBIN; COMPND 7 CHAIN: H; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: FIBRINOPEPTIDE A-ALPHA; COMPND 11 CHAIN: F, N; COMPND 12 FRAGMENT: RESIDUES 1 - 23; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: EPSILON THROMBIN; COMPND 17 CHAIN: K; COMPND 18 MOL_ID: 5; COMPND 19 MOLECULE: EPSILON THROMBIN; COMPND 20 CHAIN: M SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 TISSUE: BLOOD; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 8 ORGANISM_COMMON: CATTLE; SOURCE 9 ORGANISM_TAXID: 9913; SOURCE 10 TISSUE: BLOOD; SOURCE 11 MOL_ID: 3; SOURCE 12 MOL_ID: 4; SOURCE 13 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 14 ORGANISM_COMMON: CATTLE; SOURCE 15 ORGANISM_TAXID: 9913; SOURCE 16 TISSUE: BLOOD; SOURCE 17 MOL_ID: 5; SOURCE 18 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 19 ORGANISM_COMMON: CATTLE; SOURCE 20 ORGANISM_TAXID: 9913; SOURCE 21 TISSUE: BLOOD KEYWDS FIBRINOPEPTIDE-A, COMPLEX (SERINE PROTEASE-PEPTIDE), THROMBIN, KEYWDS 2 HYDROLASE-HYDROLASE SUBSTRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.G.MALKOWSKI,B.F.P.EDWARDS REVDAT 4 03-NOV-21 1YCP 1 SEQADV REVDAT 3 13-JUL-11 1YCP 1 VERSN REVDAT 2 24-FEB-09 1YCP 1 VERSN REVDAT 1 06-MAY-98 1YCP 0 JRNL AUTH M.G.MALKOWSKI,P.D.MARTIN,S.T.LORD,B.F.EDWARDS JRNL TITL CRYSTAL STRUCTURE OF FIBRINOGEN-AALPHA PEPTIDE 1-23 (F8Y) JRNL TITL 2 BOUND TO BOVINE THROMBIN EXPLAINS WHY THE MUTATION OF PHE-8 JRNL TITL 3 TO TYROSINE STRONGLY INHIBITS NORMAL CLEAVAGE AT ARG-16. JRNL REF BIOCHEM.J. V. 326 815 1997 JRNL REFN ISSN 0264-6021 JRNL PMID 9307032 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.D.MARTIN,M.G.MALKOWSKI,J.DIMAIO,Y.KONISHI,F.NI,B.F.EDWARDS REMARK 1 TITL BOVINE THROMBIN COMPLEXED WITH AN UNCLEAVABLE ANALOG OF REMARK 1 TITL 2 RESIDUES 7-19 OF FIBRINOGEN A ALPHA: GEOMETRY OF THE REMARK 1 TITL 3 CATALYTIC TRIAD AND INTERACTIONS OF THE P1', P2', AND P3' REMARK 1 TITL 4 SUBSTRATE RESIDUES REMARK 1 REF BIOCHEMISTRY V. 35 13030 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 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 : 16345 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) : 0.183 REMARK 3 FREE R VALUE : 0.245 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 : 4570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 276 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) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.480 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.58 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.340 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 1YCP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18614 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 7.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 63.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10900 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE 0.1M HEPES, PH REMARK 280 7.5 2.0% POLYETHYLENE GLYCOL 400 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 97.76500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.13500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.13500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 146.64750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.13500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.13500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.88250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.13500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.13500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 146.64750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.13500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.13500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.88250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 97.76500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THERE ARE TWO INDEPENDENT COMPLEXES IN THE ASYMMETRIC REMARK 300 UNIT: REMARK 300 REMARK 300 COMPLEX 1 REMARK 300 EPSILON THROMBIN: CHAINS J, K, M REMARK 300 FIBRINOPEPTIDE: CHAIN F REMARK 300 REMARK 300 COMPLEX 2 REMARK 300 ALPHA THROMBIN: CHAINS L, H REMARK 300 FIBRINOPEPTIDE: CHAIN N 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, F 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: J, K, M, N 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 1U REMARK 465 SER L 1T REMARK 465 GLU L 1S REMARK 465 ASP L 1R REMARK 465 HIS L 1Q REMARK 465 PHE L 1P REMARK 465 GLN L 1O REMARK 465 PRO L 1N REMARK 465 PHE L 1M REMARK 465 PHE L 1L REMARK 465 ASN L 1K REMARK 465 GLU L 1J REMARK 465 LYS L 1I REMARK 465 THR L 1H REMARK 465 PHE L 1G REMARK 465 GLY L 1F REMARK 465 ALA L 1E REMARK 465 GLY L 1D REMARK 465 GLU L 1C REMARK 465 ARG L 14N REMARK 465 THR H 146A REMARK 465 TRP H 146B REMARK 465 THR H 146C REMARK 465 THR H 146D REMARK 465 SER H 146E REMARK 465 VAL H 146F REMARK 465 ALA H 146G REMARK 465 GLU H 146H REMARK 465 ARG H 244 REMARK 465 LEU H 245 REMARK 465 GLY H 246 REMARK 465 SER H 247 REMARK 465 ALA F 301 REMARK 465 ASP F 302 REMARK 465 SER F 303 REMARK 465 GLY F 304 REMARK 465 GLU F 305 REMARK 465 GLY F 306 REMARK 465 ASP F 307 REMARK 465 LEU F 309 REMARK 465 ALA F 310 REMARK 465 GLU F 311 REMARK 465 GLY F 312 REMARK 465 GLY F 313 REMARK 465 ARG F 319 REMARK 465 VAL F 320 REMARK 465 VAL F 321 REMARK 465 GLU F 322 REMARK 465 ARG F 323 REMARK 465 THR J 1U REMARK 465 SER J 1T REMARK 465 GLU J 1S REMARK 465 ASP J 1R REMARK 465 HIS J 1Q REMARK 465 PHE J 1P REMARK 465 GLN J 1O REMARK 465 PRO J 1N REMARK 465 PHE J 1M REMARK 465 PHE J 1L REMARK 465 ASN J 1K REMARK 465 GLU J 1J REMARK 465 LYS J 1I REMARK 465 THR J 1H REMARK 465 PHE J 1G REMARK 465 GLY J 1F REMARK 465 ALA J 1E REMARK 465 GLY J 1D REMARK 465 GLU J 1C REMARK 465 ARG J 14N REMARK 465 THR K 147 REMARK 465 TRP K 148 REMARK 465 THR K 149 REMARK 465 THR K 150 REMARK 465 SER M 146 REMARK 465 VAL M 147 REMARK 465 ALA M 148 REMARK 465 GLU M 149 REMARK 465 ARG M 244 REMARK 465 LEU M 245 REMARK 465 GLY M 246 REMARK 465 SER M 247 REMARK 465 ALA N 301 REMARK 465 ASP N 302 REMARK 465 SER N 303 REMARK 465 GLY N 304 REMARK 465 GLU N 305 REMARK 465 GLY N 306 REMARK 465 ASP N 307 REMARK 465 LEU N 309 REMARK 465 ALA N 310 REMARK 465 GLU N 311 REMARK 465 GLY N 312 REMARK 465 GLY N 313 REMARK 465 ARG N 319 REMARK 465 VAL N 320 REMARK 465 VAL N 321 REMARK 465 GLU N 322 REMARK 465 ARG N 323 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 GLY H 186C NH1 ARG K 145 1545 1.97 REMARK 500 NE ARG H 145 O GLY M 186C 1545 2.05 REMARK 500 NE1 TRP H 60D N TYR N 308 8655 2.06 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 CYS M 182 CA - CB - SG ANGL. DEV. = 10.9 DEGREES REMARK 500 PHE M 199 N - CA - C ANGL. DEV. = -17.7 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 LEU L 6 1.30 -69.97 REMARK 500 PHE L 7 -79.65 -138.99 REMARK 500 GLN L 11 54.32 73.41 REMARK 500 GLN L 14A -38.63 -37.75 REMARK 500 GLU H 18 43.96 70.50 REMARK 500 TRP H 29 29.84 -71.76 REMARK 500 GLU H 39 138.50 -174.66 REMARK 500 CYS H 42 -163.28 -164.11 REMARK 500 SER H 48 -164.30 -174.21 REMARK 500 ASP H 62 45.14 -93.78 REMARK 500 HIS H 71 -53.13 -136.20 REMARK 500 LYS H 78 51.17 -105.59 REMARK 500 VAL H 79 -21.79 -163.50 REMARK 500 GLU H 97A -74.13 -125.01 REMARK 500 ASP H 102 74.86 -102.79 REMARK 500 PRO H 111 -179.92 -34.70 REMARK 500 HIS H 119 145.88 175.19 REMARK 500 ASN H 143 138.64 -39.63 REMARK 500 ASP H 189 170.43 178.65 REMARK 500 SER H 214 -75.51 -116.93 REMARK 500 ARG F 316 14.29 -60.03 REMARK 500 PHE J 7 -87.33 -130.72 REMARK 500 GLN J 14A -13.99 -45.27 REMARK 500 GLU J 14L 116.87 -38.30 REMARK 500 GLU K 39 130.89 -179.05 REMARK 500 CYS K 42 -158.15 -143.14 REMARK 500 SER K 48 -162.39 -166.71 REMARK 500 HIS K 71 -23.18 -149.17 REMARK 500 ARG K 77A -30.01 -34.36 REMARK 500 ARG K 93 32.89 -90.80 REMARK 500 GLU K 97A -37.06 -132.45 REMARK 500 SER K 115 -163.01 -128.53 REMARK 500 LEU K 130 79.37 -62.26 REMARK 500 ALA M 190 -160.02 -78.49 REMARK 500 CYS M 191 178.83 170.44 REMARK 500 ASN M 204B 101.76 -166.94 REMARK 500 ASN M 205 59.40 -31.50 REMARK 500 SER M 214 -76.30 -104.77 REMARK 500 ASP M 222 128.81 -39.80 REMARK 500 VAL N 315 98.54 -67.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF FIBRINOPEPTIDE A REMARK 800 -ALPHA REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN N OF FIBRINOPEPTIDE A REMARK 800 -ALPHA REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM REMARK 999 IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE REMARK 999 STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, REMARK 999 J.MOL.BIOL., V. 226, 1085). DBREF 1YCP L 1U 14N UNP P00735 THRB_BOVIN 318 366 DBREF 1YCP H 16 247 UNP P00735 THRB_BOVIN 367 625 DBREF 1YCP J 1U 14N UNP P00735 THRB_BOVIN 318 366 DBREF 1YCP K 16 150 UNP P00735 THRB_BOVIN 367 516 DBREF 1YCP M 146 247 UNP P00735 THRB_BOVIN 517 625 DBREF 1YCP F 301 323 UNP P02671 FIBA_HUMAN 20 42 DBREF 1YCP N 301 323 UNP P02671 FIBA_HUMAN 20 42 SEQADV 1YCP TYR F 308 UNP P02671 PHE ENGINEERED MUTATION SEQADV 1YCP TYR N 308 UNP P02671 PHE ENGINEERED MUTATION SEQRES 1 L 49 THR SER GLU ASP HIS PHE GLN PRO PHE PHE ASN GLU LYS SEQRES 2 L 49 THR PHE GLY ALA GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 3 L 49 LEU PHE GLU LYS LYS GLN VAL GLN ASP GLN THR GLU LYS SEQRES 4 L 49 GLU LEU PHE GLU SER TYR ILE GLU GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY GLN ASP ALA GLU VAL GLY LEU 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 VAL ASP ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG LYS VAL GLU LYS ILE SEQRES 7 H 259 SER MET LEU ASP LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP LYS GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 H 259 LEU LYS ARG PRO ILE GLU LEU SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP LYS GLN THR ALA ALA LYS LEU LEU SEQRES 11 H 259 HIS ALA GLY PHE LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 ARG ARG GLU THR TRP THR THR SER VAL ALA GLU VAL GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO LEU VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO GLY 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 TYR 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 ARG LEU GLY SER SEQRES 1 F 23 ALA ASP SER GLY GLU GLY ASP TYR LEU ALA GLU GLY GLY SEQRES 2 F 23 GLY VAL ARG GLY PRO ARG VAL VAL GLU ARG SEQRES 1 J 49 THR SER GLU ASP HIS PHE GLN PRO PHE PHE ASN GLU LYS SEQRES 2 J 49 THR PHE GLY ALA GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 3 J 49 LEU PHE GLU LYS LYS GLN VAL GLN ASP GLN THR GLU LYS SEQRES 4 J 49 GLU LEU PHE GLU SER TYR ILE GLU GLY ARG SEQRES 1 K 150 ILE VAL GLU GLY GLN ASP ALA GLU VAL GLY LEU SER PRO SEQRES 2 K 150 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 K 150 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 K 150 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 K 150 ASN PHE THR VAL ASP ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 K 150 HIS SER ARG THR ARG TYR GLU ARG LYS VAL GLU LYS ILE SEQRES 7 K 150 SER MET LEU ASP LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 K 150 TRP LYS GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 K 150 LEU LYS ARG PRO ILE GLU LEU SER ASP TYR ILE HIS PRO SEQRES 10 K 150 VAL CYS LEU PRO ASP LYS GLN THR ALA ALA LYS LEU LEU SEQRES 11 K 150 HIS ALA GLY PHE LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 K 150 ARG ARG GLU THR TRP THR THR SEQRES 1 M 109 SER VAL ALA GLU VAL GLN PRO SER VAL LEU GLN VAL VAL SEQRES 2 M 109 ASN LEU PRO LEU VAL GLU ARG PRO VAL CYS LYS ALA SER SEQRES 3 M 109 THR ARG ILE ARG ILE THR ASP ASN MET PHE CYS ALA GLY SEQRES 4 M 109 TYR LYS PRO GLY GLU GLY LYS ARG GLY ASP ALA CYS GLU SEQRES 5 M 109 GLY ASP SER GLY GLY PRO PHE VAL MET LYS SER PRO TYR SEQRES 6 M 109 ASN ASN ARG TRP TYR GLN MET GLY ILE VAL SER TRP GLY SEQRES 7 M 109 GLU GLY CYS ASP ARG ASP GLY LYS TYR GLY PHE TYR THR SEQRES 8 M 109 HIS VAL PHE ARG LEU LYS LYS TRP ILE GLN LYS VAL ILE SEQRES 9 M 109 ASP ARG LEU GLY SER SEQRES 1 N 23 ALA ASP SER GLY GLU GLY ASP TYR LEU ALA GLU GLY GLY SEQRES 2 N 23 GLY VAL ARG GLY PRO ARG VAL VAL GLU ARG FORMUL 8 HOH *276(H2 O) HELIX 1 1 GLU L 14C TYR L 14J 1 8 HELIX 2 2 ALA H 56 CYS H 58 5 3 HELIX 3 3 PRO H 60B TRP H 60D 5 3 HELIX 4 4 VAL H 61 ASP H 63 5 3 HELIX 5 5 LYS H 126 LEU H 129C 1 7 HELIX 6 6 ARG H 165 SER H 171 1 7 HELIX 7 7 PRO H 186 GLU H 186B 5 3 HELIX 8 8 VAL H 231 VAL H 241 1 11 HELIX 9 9 GLU J 14C ILE J 14K 1 9 HELIX 10 10 ALA K 56 LEU K 59 1 4 HELIX 11 11 PRO K 60B TRP K 60D 5 3 HELIX 12 12 VAL K 61 ASP K 63 5 3 HELIX 13 13 LYS K 126 LEU K 129C 1 7 HELIX 14 14 ARG M 165 SER M 171 1 7 HELIX 15 15 PRO M 186 GLU M 186B 5 3 HELIX 16 16 LYS M 235 LYS M 240 1 6 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 LYS H 107 -1 N LEU H 106 O VAL H 52 SHEET 3 B 3 ILE H 88 ILE H 90 -1 N TYR H 89 O LEU H 105 SHEET 1 C 2 LYS H 135 GLY H 140 0 SHEET 2 C 2 GLN H 156 PRO H 161 -1 N LEU H 160 O GLY H 136 SHEET 1 D 4 MET H 180 ALA H 183 0 SHEET 2 D 4 GLY H 226 HIS H 230 -1 N TYR H 228 O PHE H 181 SHEET 3 D 4 TRP H 207 GLY H 216 -1 N TRP H 215 O PHE H 227 SHEET 4 D 4 PRO H 198 LYS H 202 -1 N MET H 201 O TYR H 208 SHEET 1 E 3 LEU K 64 ARG K 67 0 SHEET 2 E 3 GLN K 30 ARG K 35 -1 N PHE K 34 O LEU K 65 SHEET 3 E 3 GLU K 39 SER K 45 -1 N ALA K 44 O VAL K 31 SHEET 1 F 3 TRP K 51 THR K 54 0 SHEET 2 F 3 ALA K 104 LEU K 108 -1 N LEU K 106 O VAL K 52 SHEET 3 F 3 LEU K 85 ILE K 90 -1 N TYR K 89 O LEU K 105 SHEET 1 G 4 MET M 180 ALA M 183 0 SHEET 2 G 4 GLY M 226 HIS M 230 -1 N TYR M 228 O PHE M 181 SHEET 3 G 4 ARG M 206 TRP M 215 -1 N TRP M 215 O PHE M 227 SHEET 4 G 4 PRO M 198 SER M 203 -1 N SER M 203 O ARG M 206 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.04 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.00 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.05 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.02 SSBOND 5 CYS J 1 CYS K 122 1555 1555 2.04 SSBOND 6 CYS K 42 CYS K 58 1555 1555 2.02 SSBOND 7 CYS M 168 CYS M 182 1555 1555 2.01 SSBOND 8 CYS M 191 CYS M 220 1555 1555 2.03 CISPEP 1 SER H 36A PRO H 37 0 -0.34 CISPEP 2 SER K 36A PRO K 37 0 -0.86 SITE 1 AC1 23 HOH F 450 HOH F 481 HOH F 482 HOH F 668 SITE 2 AC1 23 LEU H 41 HIS H 57 TYR H 60A TRP H 96 SITE 3 AC1 23 LYS H 97 GLU H 97A LEU H 99 ILE H 174 SITE 4 AC1 23 ASP H 189 ALA H 190 CYS H 191 GLU H 192 SITE 5 AC1 23 GLY H 193 SER H 195 SER H 214 TRP H 215 SITE 6 AC1 23 GLY H 216 GLY H 219 HOH H 411 SITE 1 AC2 16 TRP H 60D HOH H 504 HIS K 57 LYS K 97 SITE 2 AC2 16 GLU K 97A HOH K 442 HOH K 495 ILE M 174 SITE 3 AC2 16 ASP M 189 GLU M 192 GLY M 193 SER M 195 SITE 4 AC2 16 SER M 214 TRP M 215 GLY M 216 GLY M 219 CRYST1 88.270 88.270 195.530 90.00 90.00 90.00 P 43 21 2 16 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 0.011329 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011329 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005114 0.00000