HEADER BLOOD CLOTTING 27-AUG-03 1QVH OBSLTE 02-MAY-06 1QVH 2A45 TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THROMBIN AND THE TITLE 2 CENTRAL "E" REGION OF FIBRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: B, E; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PPACK THROMBIN INHIBITOR; COMPND 13 CHAIN: C, F; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: D-PHE-PRO-ARG CHLOROMETHYLKETONE (PPACK) COMPND 16 WITH CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: FIBRIN ALPHA-E CHAIN; COMPND 19 CHAIN: G, J; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: FIBRIN BETA CHAIN; COMPND 22 CHAIN: H, K; COMPND 23 MOL_ID: 6; COMPND 24 MOLECULE: FIBRINOGEN GAMMA CHAIN; COMPND 25 CHAIN: I, L; COMPND 26 SYNONYM: PRO2061 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: THE INHIBITOR WAS CHEMICALLY SYNTHESIZED.; SOURCE 10 MOL_ID: 4; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 OTHER_DETAILS: PROTEOLYTIC FRAGMENT; SOURCE 14 MOL_ID: 5; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 OTHER_DETAILS: PROTEOLYTIC FRAGMENT; SOURCE 18 MOL_ID: 6; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_COMMON: HUMAN; SOURCE 21 OTHER_DETAILS: PROTEOLYTIC FRAGMENT KEYWDS THROMBIN, FIBRIN, FRAGMENT E, THROMBIN-FIBRIN COMPLEX, KEYWDS 2 COILED COILS, DISULFIDE RINGS, PPACK EXPDTA X-RAY DIFFRACTION AUTHOR I.PECHIK,J.MADRAZO,G.L.GILLILAND,L.MEDVED REVDAT 2 02-MAY-06 1QVH 1 OBSLTE REVDAT 1 02-MAR-04 1QVH 0 JRNL AUTH I.PECHIK,J.MADRAZO,M.W.MOSESSON,I.HERNANDEZ, JRNL AUTH 2 G.L.GILLILAND,L.MEDVED JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THROMBIN JRNL TITL 2 AND THE CENTRAL "E" REGION OF FIBRIN JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 2718 2004 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 3.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.222 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2390 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 25847 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6782 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: FLAT MODEL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DIFFRACTION DATA WERE COLLECTED FROM REMARK 3 MEROHEDRALLY TWINNED CRYSTAL. THE PRESENCE OF 38.2% TWIN REMARK 3 FRACTION CORRESPONDING TO -H -H-K -L TWINNING OPERATOR WAS REMARK 3 TAKEN INTO ACCOUNT IN THE REFINEMENT. REMARK 4 REMARK 4 1QVH COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-19) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-2003. REMARK 100 THE RCSB ID CODE IS RCSB020117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.90 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26890 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.650 REMARK 200 RESOLUTION RANGE LOW (A) : 31.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 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 : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: 1PPB, 1JY2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3500, AMMONIUM PHOSPHATE, TRIS, REMARK 280 PH 7.9, MICRODIALYSIS, TEMPERATURE 298.0K, PH 7.90 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,1/3+Z REMARK 290 3555 -X+Y,-X,2/3+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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.15067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 128.30133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 12CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, REMARK 350 J, K, L 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 A -3 REMARK 465 PHE A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLU B 247 REMARK 465 THR D -3 REMARK 465 PHE D -2 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 GLU E 247 REMARK 465 GLY G 17 REMARK 465 PRO G 18 REMARK 465 ARG G 19 REMARK 465 VAL G 20 REMARK 465 VAL G 21 REMARK 465 GLU G 22 REMARK 465 ARG G 23 REMARK 465 HIS G 24 REMARK 465 GLN G 25 REMARK 465 SER G 26 REMARK 465 ALA G 27 REMARK 465 CYS G 28 REMARK 465 LYS G 29 REMARK 465 ASP G 30 REMARK 465 SER G 31 REMARK 465 GLY H 15 REMARK 465 HIS H 16 REMARK 465 ARG H 17 REMARK 465 PRO H 18 REMARK 465 LEU H 19 REMARK 465 ASP H 20 REMARK 465 LYS H 21 REMARK 465 LYS H 22 REMARK 465 ARG H 23 REMARK 465 GLU H 24 REMARK 465 GLU H 25 REMARK 465 ALA H 26 REMARK 465 PRO H 27 REMARK 465 SER H 28 REMARK 465 LEU H 29 REMARK 465 ARG H 30 REMARK 465 PRO H 31 REMARK 465 ALA H 32 REMARK 465 PRO H 33 REMARK 465 PRO H 34 REMARK 465 PRO H 35 REMARK 465 ILE H 36 REMARK 465 SER H 37 REMARK 465 GLY H 38 REMARK 465 GLY H 39 REMARK 465 GLY H 40 REMARK 465 TYR H 41 REMARK 465 ARG H 42 REMARK 465 ALA H 43 REMARK 465 ARG H 44 REMARK 465 PRO H 45 REMARK 465 ALA H 46 REMARK 465 LYS H 47 REMARK 465 ALA H 48 REMARK 465 ALA H 49 REMARK 465 ALA H 50 REMARK 465 THR H 51 REMARK 465 GLN H 52 REMARK 465 LYS H 53 REMARK 465 LYS H 54 REMARK 465 VAL H 55 REMARK 465 TYR I 1 REMARK 465 VAL I 2 REMARK 465 ALA I 3 REMARK 465 THR I 4 REMARK 465 ARG I 5 REMARK 465 GLY J 17 REMARK 465 PRO J 18 REMARK 465 ARG J 19 REMARK 465 VAL J 20 REMARK 465 VAL J 21 REMARK 465 GLU J 22 REMARK 465 ARG J 23 REMARK 465 HIS J 24 REMARK 465 GLN J 25 REMARK 465 SER J 26 REMARK 465 ALA J 27 REMARK 465 CYS J 28 REMARK 465 LYS J 29 REMARK 465 ASP J 30 REMARK 465 SER J 31 REMARK 465 GLY K 15 REMARK 465 HIS K 16 REMARK 465 ARG K 17 REMARK 465 PRO K 18 REMARK 465 LEU K 19 REMARK 465 ASP K 20 REMARK 465 LYS K 21 REMARK 465 LYS K 22 REMARK 465 ARG K 23 REMARK 465 GLU K 24 REMARK 465 GLU K 25 REMARK 465 ALA K 26 REMARK 465 PRO K 27 REMARK 465 SER K 28 REMARK 465 LEU K 29 REMARK 465 ARG K 30 REMARK 465 PRO K 31 REMARK 465 ALA K 32 REMARK 465 PRO K 33 REMARK 465 PRO K 34 REMARK 465 PRO K 35 REMARK 465 ILE K 36 REMARK 465 SER K 37 REMARK 465 GLY K 38 REMARK 465 GLY K 39 REMARK 465 GLY K 40 REMARK 465 TYR K 41 REMARK 465 ARG K 42 REMARK 465 ALA K 43 REMARK 465 ARG K 44 REMARK 465 PRO K 45 REMARK 465 ALA K 46 REMARK 465 LYS K 47 REMARK 465 ALA K 48 REMARK 465 ALA K 49 REMARK 465 ALA K 50 REMARK 465 THR K 51 REMARK 465 GLN K 52 REMARK 465 LYS K 53 REMARK 465 LYS K 54 REMARK 465 VAL K 55 REMARK 465 TYR L 1 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 LYS B 36 CG CD CE NZ REMARK 470 LYS B 109 CG CD CE NZ REMARK 470 ARG B 126 CG CD NE CZ NH1 NH2 REMARK 470 LYS E 36 CG CD CE NZ REMARK 470 LYS E 109 CG CD CE NZ REMARK 470 ARG E 126 CG CD NE CZ NH1 NH2 REMARK 470 LEU G 73 CG CD1 CD2 REMARK 470 GLU H 84 CG CD OE1 OE2 REMARK 470 GLN H 88 CG CD OE1 NE2 REMARK 470 LEU H 100 CG CD1 CD2 REMARK 470 LYS I 35 CG CD CE NZ REMARK 470 LEU J 73 CG CD1 CD2 REMARK 470 GLU K 84 CG CD OE1 OE2 REMARK 470 GLN K 88 CG CD OE1 NE2 REMARK 470 LEU K 100 CG CD1 CD2 REMARK 470 LYS L 35 CG CD CE NZ 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 REMARK 500 O LYS I 35 OD2 ASP I 39 2.03 REMARK 500 O ASP H 98 OD1 ASN H 101 2.09 REMARK 500 OG SER E 195 O ARM F 3 2.17 REMARK 500 O VAL H 97 ND2 ASN H 101 2.18 REMARK 500 O GLN I 41 OD2 ASP I 45 2.19 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER B 36A CB SER B 36A OG 0.086 REMARK 500 ARG B 77A CG ARG B 77A CD 0.089 REMARK 500 ILE D 14K CA ILE D 14K CB 0.092 REMARK 500 MET J 51 SD MET J 51 CE -0.110 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY B 43 N - CA - C ANGL. DEV. =-14.9 DEGREES REMARK 500 GLY E 43 N - CA - C ANGL. DEV. =-11.1 DEGREES REMARK 500 THR E 147 N - CA - C ANGL. DEV. = 11.3 DEGREES REMARK 500 PHE E 199 N - CA - C ANGL. DEV. =-12.9 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ILE A 14K -67.74 65.89 REMARK 500 PHE D 7 -106.06 -159.93 REMARK 500 ILE D 14K -68.78 67.14 REMARK 500 ASN E 78 -45.75 67.90 REMARK 500 LYS E 145 -134.28 161.67 REMARK 999 REMARK 999 SEQUENCE REMARK 999 HUMAN ALPHA THROMBIN COMPRISES AMINO ACID RESIDUES 1H TO 247 REMARK 999 (CHYMOTRYPSIN NUMBERING). N-TERMINAL SEQUENCES OF THE REMARK 999 CENTRAL "E" REGION OF HUMAN FIBRIN START FROM RESIDUE 17 REMARK 999 FOR ALPHA CHAINS (CHAINS G, J), 15 FOR BETA CHAINS (CHAINS REMARK 999 H, K), AND 1 FOR GAMMA CHAINS (CHAINS I, L). C-TERMINAL REMARK 999 SEQUENCES OF ALPHA, BETA, AND GAMMA CHAINS WERE NOT REMARK 999 DETERMINED. DUE TO THE LACK OF ELECTRON DENSITY THROMBIN REMARK 999 RESIDUES 1H THROUGH 1E AND RESIDUE 247 COULD NOT BE BUILD, REMARK 999 AS WELL AS RESIDUES 17 THROUGH 31 OF FIBRIN ALPHA CHAINS, REMARK 999 15 THROUGH 55 OF FIBRIN BETA CHAINS, AND 1 THROUGH 5 OF REMARK 999 FIBRIN GAMMA CHAINS. REMARK 999 REMARK 999 MISSING ATOMS: REMARK 999 THE FOLLOWING RESIDUES DID NOT DISPLAY ELECTRON DENSITY FOR REMARK 999 THE SIDE CHAINS OF: REMARK 999 CHAIN B: LYS 36, LYS 109, ARG 126. REMARK 999 CHAIN E: LYS 36, LYS 109, ARG 126. REMARK 999 CHAIN H: GLU 84, GLN 88. REMARK 999 CHAIN I: LYS 35. REMARK 999 CHAIN K: GLU 84, GLN 88. REMARK 999 CHAIN L: LYS 35. DBREF 1QVH A 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1QVH D 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1QVH B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1QVH E 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1QVH G 17 73 UNP P02671 FIBA_HUMAN 36 92 DBREF 1QVH J 17 73 UNP P02671 FIBA_HUMAN 36 92 DBREF 1QVH H 15 105 UNP P02675 FIBB_HUMAN 45 135 DBREF 1QVH K 15 105 UNP P02675 FIBB_HUMAN 45 135 DBREF 1QVH I 1 45 UNP P02679 FIBG_HUMAN 27 71 DBREF 1QVH L 1 45 UNP P02679 FIBG_HUMAN 27 71 SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 A 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 C 3 DPN PRO ARM SEQRES 1 D 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 D 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 D 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 E 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 E 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 E 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 E 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 E 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 E 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 E 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 E 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 E 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 E 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 E 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 E 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 E 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 E 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 E 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 E 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 E 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 E 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 E 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 E 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 F 3 DPN PRO ARM SEQRES 1 G 57 GLY PRO ARG VAL VAL GLU ARG HIS GLN SER ALA CYS LYS SEQRES 2 G 57 ASP SER ASP TRP PRO PHE CYS SER ASP GLU ASP TRP ASN SEQRES 3 G 57 TYR LYS CYS PRO SER GLY CYS ARG MET LYS GLY LEU ILE SEQRES 4 G 57 ASP GLU VAL ASN GLN ASP PHE THR ASN ARG ILE ASN LYS SEQRES 5 G 57 LEU LYS ASN SER LEU SEQRES 1 H 91 GLY HIS ARG PRO LEU ASP LYS LYS ARG GLU GLU ALA PRO SEQRES 2 H 91 SER LEU ARG PRO ALA PRO PRO PRO ILE SER GLY GLY GLY SEQRES 3 H 91 TYR ARG ALA ARG PRO ALA LYS ALA ALA ALA THR GLN LYS SEQRES 4 H 91 LYS VAL GLU ARG LYS ALA PRO ASP ALA GLY GLY CYS LEU SEQRES 5 H 91 HIS ALA ASP PRO ASP LEU GLY VAL LEU CYS PRO THR GLY SEQRES 6 H 91 CYS GLN LEU GLN GLU ALA LEU LEU GLN GLN GLU ARG PRO SEQRES 7 H 91 ILE ARG ASN SER VAL ASP GLU LEU ASN ASN ASN VAL GLU SEQRES 1 I 45 TYR VAL ALA THR ARG ASP ASN CYS CYS ILE LEU ASP GLU SEQRES 2 I 45 ARG PHE GLY SER TYR CYS PRO THR THR CYS GLY ILE ALA SEQRES 3 I 45 ASP PHE LEU SER THR TYR GLN THR LYS VAL ASP LYS ASP SEQRES 4 I 45 LEU GLN SER LEU GLU ASP SEQRES 1 J 57 GLY PRO ARG VAL VAL GLU ARG HIS GLN SER ALA CYS LYS SEQRES 2 J 57 ASP SER ASP TRP PRO PHE CYS SER ASP GLU ASP TRP ASN SEQRES 3 J 57 TYR LYS CYS PRO SER GLY CYS ARG MET LYS GLY LEU ILE SEQRES 4 J 57 ASP GLU VAL ASN GLN ASP PHE THR ASN ARG ILE ASN LYS SEQRES 5 J 57 LEU LYS ASN SER LEU SEQRES 1 K 91 GLY HIS ARG PRO LEU ASP LYS LYS ARG GLU GLU ALA PRO SEQRES 2 K 91 SER LEU ARG PRO ALA PRO PRO PRO ILE SER GLY GLY GLY SEQRES 3 K 91 TYR ARG ALA ARG PRO ALA LYS ALA ALA ALA THR GLN LYS SEQRES 4 K 91 LYS VAL GLU ARG LYS ALA PRO ASP ALA GLY GLY CYS LEU SEQRES 5 K 91 HIS ALA ASP PRO ASP LEU GLY VAL LEU CYS PRO THR GLY SEQRES 6 K 91 CYS GLN LEU GLN GLU ALA LEU LEU GLN GLN GLU ARG PRO SEQRES 7 K 91 ILE ARG ASN SER VAL ASP GLU LEU ASN ASN ASN VAL GLU SEQRES 1 L 45 TYR VAL ALA THR ARG ASP ASN CYS CYS ILE LEU ASP GLU SEQRES 2 L 45 ARG PHE GLY SER TYR CYS PRO THR THR CYS GLY ILE ALA SEQRES 3 L 45 ASP PHE LEU SER THR TYR GLN THR LYS VAL ASP LYS ASP SEQRES 4 L 45 LEU GLN SER LEU GLU ASP MODRES 1QVH DPN C 1 PHE D-PHENYLALANINE MODRES 1QVH ARM C 3 ARG DEOXY-METHYL-ARGININE MODRES 1QVH DPN F 1 PHE D-PHENYLALANINE MODRES 1QVH ARM F 3 ARG DEOXY-METHYL-ARGININE HET DPN C 1 11 HET ARM C 3 12 HET DPN F 1 11 HET ARM F 3 12 HET PO4 1 5 HET PO4 2 5 HETNAM DPN D-PHENYLALANINE HETNAM ARM DEOXY-METHYL-ARGININE HETNAM PO4 PHOSPHATE ION FORMUL 3 DPN 2(C9 H11 N O2) FORMUL 3 ARM 2(C7 H16 N4 O) FORMUL 13 PO4 2(O4 P 3-) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 GLU A 14C TYR A 14J 1 8 HELIX 3 3 ALA B 55 LEU B 59 5 5 HELIX 4 4 TYR B 60A ASP B 60E 5 5 HELIX 5 5 THR B 60I ASN B 62 5 3 HELIX 6 6 ASP B 125 LEU B 130 1 9 HELIX 7 7 GLU B 164 THR B 172 1 9 HELIX 8 8 PRO B 204 ASN B 205 5 4 HELIX 9 9 VAL B 231 GLY B 246 1 16 HELIX 10 10 GLU D 14C SER D 14I 1 7 HELIX 11 11 ALA E 55 LEU E 59 5 5 HELIX 12 12 TYR E 60A ASP E 60E 5 5 HELIX 13 13 THR E 60I ASN E 62 5 3 HELIX 14 14 ASP E 125 LEU E 130 1 9 HELIX 15 15 GLU E 164 THR E 172 1 9 HELIX 16 16 PRO E 204 ASN E 205 5 4 HELIX 17 17 VAL E 231 GLY E 246 1 16 HELIX 18 18 SER G 47 SER G 72 1 26 HELIX 19 19 THR H 78 GLU H 105 1 28 HELIX 20 20 THR I 21 ASP I 45 1 25 HELIX 21 21 SER J 47 SER J 72 1 26 HELIX 22 22 THR K 78 GLU K 105 1 28 HELIX 23 23 ASP L 12 GLY L 16 5 5 HELIX 24 24 THR L 21 ASP L 45 1 25 SHEET 1 A 7 LYS B 81 SER B 83 0 SHEET 2 A 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 3 A 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 4 A 7 GLU B 39 SER B 48 -1 O GLU B 39 N ARG B 35 SHEET 5 A 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 6 A 7 ALA B 104 LEU B 108 -1 O ALA B 104 N THR B 54 SHEET 7 A 7 LEU B 85 ILE B 90 -1 N TYR B 89 O LEU B 105 SHEET 1 B 2 GLY B 136 GLY B 140 0 SHEET 2 B 2 GLN B 156 LEU B 160 -1 O LEU B 160 N GLY B 136 SHEET 1 C 3 PRO B 198 PHE B 199 0 SHEET 2 C 3 GLY B 211 TRP B 215 -1 O GLY B 211 N PHE B 199 SHEET 3 C 3 PHE B 227 HIS B 230 -1 O PHE B 227 N TRP B 215 SHEET 1 D 2 LYS B 202 SER B 203 0 SHEET 2 D 2 ARG B 206 TRP B 207 -1 O ARG B 206 N SER B 203 SHEET 1 E 7 LYS E 81 SER E 83 0 SHEET 2 E 7 LEU E 64 ILE E 68 -1 N ILE E 68 O LYS E 81 SHEET 3 E 7 GLN E 30 ARG E 35 -1 N PHE E 34 O LEU E 65 SHEET 4 E 7 GLU E 39 SER E 48 -1 O GLU E 39 N ARG E 35 SHEET 5 E 7 TRP E 51 THR E 54 -1 O LEU E 53 N SER E 45 SHEET 6 E 7 ALA E 104 LEU E 108 -1 O ALA E 104 N THR E 54 SHEET 7 E 7 LEU E 85 ILE E 90 -1 N TYR E 89 O LEU E 105 SHEET 1 F 2 GLY E 136 GLY E 140 0 SHEET 2 F 2 GLN E 156 LEU E 160 -1 O LEU E 160 N GLY E 136 SHEET 1 G 3 PRO E 198 SER E 203 0 SHEET 2 G 3 ARG E 206 TRP E 215 -1 O ARG E 206 N SER E 203 SHEET 3 G 3 PHE E 227 HIS E 230 -1 O PHE E 227 N TRP E 215 SHEET 1 H 3 LYS G 44 CYS G 45 0 SHEET 2 H 3 GLY K 73 PRO K 77 -1 O CYS K 76 N CYS G 45 SHEET 3 H 3 CYS K 65 HIS K 67 -1 N HIS K 67 O GLY K 73 SHEET 1 I 3 CYS H 65 HIS H 67 0 SHEET 2 I 3 GLY H 73 PRO H 77 -1 O LEU H 75 N CYS H 65 SHEET 3 I 3 LYS J 44 CYS J 45 -1 O CYS J 45 N CYS H 76 SHEET 1 J 2 CYS I 19 PRO I 20 0 SHEET 2 J 2 TYR L 18 CYS L 19 -1 O CYS L 19 N CYS I 19 SSBOND 1 CYS A 1 CYS B 122 SSBOND 2 CYS B 42 CYS B 58 SSBOND 3 CYS B 168 CYS B 182 SSBOND 4 CYS B 191 CYS B 220 SSBOND 5 CYS D 1 CYS E 122 SSBOND 6 CYS E 42 CYS E 58 SSBOND 7 CYS E 168 CYS E 182 SSBOND 8 CYS E 191 CYS E 220 SSBOND 9 CYS G 36 CYS K 65 SSBOND 10 CYS G 45 CYS I 23 SSBOND 11 CYS G 49 CYS H 76 SSBOND 12 CYS H 65 CYS J 36 SSBOND 13 CYS H 80 CYS I 19 SSBOND 14 CYS I 8 CYS L 9 SSBOND 15 CYS I 9 CYS L 8 SSBOND 16 CYS J 45 CYS L 23 SSBOND 17 CYS J 49 CYS K 76 SSBOND 18 CYS K 80 CYS L 19 LINK OG SER B 195 C ARM C 3 LINK OG SER E 195 C ARM F 3 LINK NE2 HIS B 57 CM ARM C 3 LINK NE2 HIS E 57 CM ARM F 3 CISPEP 1 SER B 36A PRO B 37 0 -0.99 CISPEP 2 SER E 36A PRO E 37 0 -0.15 CRYST1 76.263 76.263 192.452 90.00 90.00 120.00 P 31 6 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 0.013113 0.007571 0.000000 0.00000 SCALE2 0.000000 0.015141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005196 0.00000