PDB Short entry for 1NY2 HEADER HYDROLASE/HYDROLASE INHIBITOR 11-FEB-03 1NY2 TITLE HUMAN ALPHA THROMBIN INHIBITED BY RPPGF AND HIRUGEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: 1; COMPND 4 FRAGMENT: LIGHT CHAIN A; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 9 CHAIN: 2; COMPND 10 FRAGMENT: HEAVY CHAIN B; COMPND 11 SYNONYM: COAGULATION FACTOR II; COMPND 12 EC: 3.4.21.5; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HIRUGEN; COMPND 15 CHAIN: 3; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: INHIBITOR PEPTIDE RPPGF; COMPND 19 CHAIN: 4; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: ALPHA THROMBIN CATALYTIC DOMAIN; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS THROMBOSIS, RETRO BINDING, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.KRISHNAN,A.TULINSKY,A.H.SCHMAIER,A.A.HASAN,M.WARNOCK,S.SRIKANTH, AUTHOR 2 F.MAHDI REVDAT 7 16-AUG-23 1NY2 1 LINK REVDAT 6 11-OCT-17 1NY2 1 REMARK REVDAT 5 25-MAR-15 1NY2 1 DBREF REVDAT 4 13-JUL-11 1NY2 1 VERSN REVDAT 3 24-FEB-09 1NY2 1 VERSN REVDAT 2 05-APR-05 1NY2 1 JRNL REVDAT 1 04-MAR-03 1NY2 0 JRNL AUTH A.A.HASAN,M.WARNOCK,M.NIEMAN,S.SRIKANTH,F.MAHDI,R.KRISHNAN, JRNL AUTH 2 A.TULINSKY,A.H.SCHMAIER JRNL TITL MECHANISMS OF ARG-PRO-PRO-GLY-PHE INHIBITION OF THROMBIN. JRNL REF AM.J.PHYSIOL.HEART V. 285 H183 2003 JRNL REF 2 CIRC.PHYSIOL. JRNL REFN ISSN 0363-6135 JRNL PMID 12598231 JRNL DOI 10.1152/AJPHEART.00490.2002 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16037 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 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 : 2503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 51 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) : 0.020 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.047 ; 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) : 0.057 ; 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 1NY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.6 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 : YALE MIRRORS REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17158 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06800 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 0.5 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1DIT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM SULPHATE, SODIUM REMARK 280 ACETATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 25K, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 39.57500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.48500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.57500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.48500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2, 3, 4 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 PHE 4 384 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 OG SER 2 195 N ARG 4 380 2.08 REMARK 500 O PHE 1 1G N GLY 1 1D 2.10 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 ARG 2 75 NE ARG 2 75 CZ 0.080 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 GLY 1 1F N - CA - C ANGL. DEV. = -16.0 DEGREES REMARK 500 GLY 1 1F O - C - N ANGL. DEV. = 10.6 DEGREES REMARK 500 GLU 1 1C CA - CB - CG ANGL. DEV. = 20.1 DEGREES REMARK 500 ASP 1 1A CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 CYS 1 1 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 LEU 1 3 O - C - N ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG 1 4 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 SER 1 11 N - CA - CB ANGL. DEV. = 9.4 DEGREES REMARK 500 GLU 1 13 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG 1 14D NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 GLU 1 14E CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG 1 15 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ASP 2 21 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 GLN 2 30 N - CA - CB ANGL. DEV. = 11.1 DEGREES REMARK 500 LEU 2 33 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG 2 35 CD - NE - CZ ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG 2 35 NH1 - CZ - NH2 ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG 2 35 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG 2 35 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 LEU 2 41 CB - CA - C ANGL. DEV. = 13.3 DEGREES REMARK 500 ASP 2 49 CB - CG - OD1 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG 2 50 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG 2 50 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 TYR 2 60A CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 TRP 2 60D O - C - N ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP 2 60E CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 LEU 2 65 N - CA - CB ANGL. DEV. = 13.1 DEGREES REMARK 500 LEU 2 65 CA - CB - CG ANGL. DEV. = 20.5 DEGREES REMARK 500 ARG 2 73 CD - NE - CZ ANGL. DEV. = -17.2 DEGREES REMARK 500 ARG 2 73 NE - CZ - NH1 ANGL. DEV. = -11.9 DEGREES REMARK 500 ARG 2 73 NE - CZ - NH2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG 2 75 CG - CD - NE ANGL. DEV. = 39.0 DEGREES REMARK 500 ARG 2 75 CD - NE - CZ ANGL. DEV. = 42.9 DEGREES REMARK 500 ARG 2 75 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG 2 75 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 TYR 2 76 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 GLU 2 77 CB - CG - CD ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG 2 77A CD - NE - CZ ANGL. DEV. = 20.2 DEGREES REMARK 500 ARG 2 77A NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 HIS 2 91 CA - CB - CG ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG 2 93 CD - NE - CZ ANGL. DEV. = 11.0 DEGREES REMARK 500 TYR 2 94 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASN 2 95 N - CA - CB ANGL. DEV. = 16.2 DEGREES REMARK 500 ARG 2 97 CD - NE - CZ ANGL. DEV. = 11.0 DEGREES REMARK 500 MET 2 106 CG - SD - CE ANGL. DEV. = -9.7 DEGREES REMARK 500 VAL 2 112 O - C - N ANGL. DEV. = 9.6 DEGREES REMARK 500 PHE 2 114 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 LEU 2 123 O - C - N ANGL. DEV. = 12.0 DEGREES REMARK 500 GLY 2 136 C - N - CA ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG 2 137 CD - NE - CZ ANGL. DEV. = 12.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 92 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 1 1G -157.14 -145.75 REMARK 500 GLU 1 1C -104.56 -31.97 REMARK 500 ALA 1 1B -37.89 -172.60 REMARK 500 LEU 1 6 -9.83 -52.02 REMARK 500 PHE 1 7 -94.66 -123.31 REMARK 500 TYR 1 14J 37.33 -78.46 REMARK 500 ILE 1 14K -66.57 106.26 REMARK 500 SER 2 36A 129.75 -173.46 REMARK 500 CYS 2 42 -169.32 -164.93 REMARK 500 ASN 2 60G 72.87 -174.09 REMARK 500 ARG 2 77A -72.96 -21.20 REMARK 500 ARG 2 97 7.17 -47.25 REMARK 500 GLU 2 97A -78.41 -140.80 REMARK 500 ARG 2 101 71.51 67.22 REMARK 500 HIS 2 119 138.63 -177.76 REMARK 500 ASN 2 204B 10.30 -162.02 REMARK 500 SER 2 214 -85.02 -103.44 REMARK 500 ASP 2 243 -72.45 -67.22 REMARK 500 GLU 3 61 46.47 -71.96 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 ARG 2 233 0.14 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 GLU 2 192 11.02 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 3 OF HIRUGEN REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HDT RELATED DB: PDB REMARK 900 STRUCTURE OF A RETRO-BINDING PEPTIDE INHIBITOR COMPLEXED WITH HUMAN- REMARK 900 THROMBIN REMARK 900 RELATED ID: 7KME RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN -THROMBIN INHIBITED WITH SEL2711 REMARK 900 RELATED ID: 8KME RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN -THROMBIN INHIBITED WITH SEL2770 REMARK 900 RELATED ID: 1TMU RELATED DB: PDB REMARK 900 CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES AND REMARK 900 HUMAN -THROMBIN DUE TO DIFFERENT CRYSTAL FORMS DBREF 1NY2 1 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1NY2 2 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1NY2 3 55 64 UNP P28504 HIR2_HIRME 55 64 DBREF 1NY2 4 380 384 PDB 1NY2 1NY2 380 384 SEQRES 1 1 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 1 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 1 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 2 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 2 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 2 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 2 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 2 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 2 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 2 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 2 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 2 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 2 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 2 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 2 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 2 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 2 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 2 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 2 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 2 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 2 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 2 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 2 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 3 10 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU SEQRES 1 4 5 ARG PRO PRO GLY PHE MODRES 1NY2 TYS 3 63 TYR O-SULFO-L-TYROSINE HET TYS 3 63 16 HETNAM TYS O-SULFO-L-TYROSINE FORMUL 3 TYS C9 H11 N O6 S FORMUL 5 HOH *51(H2 O) HELIX 1 1 GLU 1 14C GLU 1 14H 1 6 HELIX 2 2 ALA 2 55 CYS 2 58 5 4 HELIX 3 3 PRO 2 60B ASP 2 60E 5 4 HELIX 4 4 THR 2 60I ASN 2 62 5 3 HELIX 5 5 ASP 2 125 LEU 2 130 1 9 HELIX 6 6 GLU 2 164 ASP 2 170 1 7 HELIX 7 7 LYS 2 185 GLY 2 186C 5 5 HELIX 8 8 LEU 2 234 GLY 2 246 1 13 SHEET 1 A 7 SER 2 20 ASP 2 21 0 SHEET 2 A 7 GLN 2 156 PRO 2 161 -1 O VAL 2 157 N SER 2 20 SHEET 3 A 7 LYS 2 135 GLY 2 140 -1 N VAL 2 138 O VAL 2 158 SHEET 4 A 7 PRO 2 198 LYS 2 202 -1 O VAL 2 200 N ARG 2 137 SHEET 5 A 7 TRP 2 207 TRP 2 215 -1 O MET 2 210 N PHE 2 199 SHEET 6 A 7 GLY 2 226 THR 2 229 -1 O PHE 2 227 N TRP 2 215 SHEET 7 A 7 MET 2 180 ALA 2 183 -1 N PHE 2 181 O TYR 2 228 SHEET 1 B 7 GLN 2 30 ARG 2 35 0 SHEET 2 B 7 GLU 2 39 LEU 2 46 -1 O GLU 2 39 N ARG 2 35 SHEET 3 B 7 TRP 2 51 THR 2 54 -1 O LEU 2 53 N SER 2 45 SHEET 4 B 7 ALA 2 104 LEU 2 108 -1 O ALA 2 104 N THR 2 54 SHEET 5 B 7 LYS 2 81 ILE 2 90 -1 N TYR 2 89 O LEU 2 105 SHEET 6 B 7 LEU 2 64 ILE 2 68 -1 N VAL 2 66 O SER 2 83 SHEET 7 B 7 GLN 2 30 ARG 2 35 -1 N MET 2 32 O ARG 2 67 SSBOND 1 CYS 1 1 CYS 2 122 1555 1555 2.09 SSBOND 2 CYS 2 42 CYS 2 58 1555 1555 2.04 SSBOND 3 CYS 2 168 CYS 2 182 1555 1555 2.14 SSBOND 4 CYS 2 191 CYS 2 220 1555 1555 2.07 LINK C GLU 3 62 N TYS 3 63 1555 1555 1.31 LINK C TYS 3 63 N LEU 3 64 1555 1555 1.33 CISPEP 1 SER 2 36A PRO 2 37 0 -5.14 SITE 1 AC1 14 PHE 2 34 LYS 2 36 LEU 2 65 ARG 2 67 SITE 2 AC1 14 ARG 2 73 THR 2 74 TYR 2 76 ILE 2 82 SITE 3 AC1 14 GLU 2 97A ASN 2 98 ASP 2 100 ARG 2 175 SITE 4 AC1 14 HOH 3 423 HOH 3 429 CRYST1 79.150 104.970 45.180 90.00 90.00 90.00 P 21 21 2 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 0.012634 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022134 0.00000