HEADER BLOOD CLOTTING/HYDROLASE INHIBITOR 11-DEC-98 1VR1 TITLE SPECIFITY FOR PLASMINOGEN ACTIVATOR INHIBITOR-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN; COMPND 9 CHAIN: H; COMPND 10 SYNONYM: COAGULATION FACTOR II; COMPND 11 EC: 3.4.21.5; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HIRUDIN; COMPND 15 CHAIN: I; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F2; SOURCE 6 EXPRESSION_SYSTEM: CRICETINAE GEN. SP.; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 36483; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: F2; SOURCE 13 EXPRESSION_SYSTEM: CRICETINAE GEN. SP.; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 36483; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 17 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 18 ORGANISM_TAXID: 6421; SOURCE 19 EXPRESSION_SYSTEM: CRICETINAE GEN. SP.; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 36483 KEYWDS THROMBIN, BLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.J.DEKKER,A.EICHINGER,A.A.STOOP,W.BODE,H.PANNEKOEK,A.J.G.HORREVOETS REVDAT 6 21-DEC-22 1VR1 1 SEQADV LINK REVDAT 5 13-JUL-11 1VR1 1 VERSN REVDAT 4 24-FEB-09 1VR1 1 VERSN REVDAT 3 05-APR-05 1VR1 1 JRNL REMARK REVDAT 2 29-DEC-99 1VR1 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 29-DEC-99 1VR1 0 JRNL AUTH R.J.DEKKER,A.EICHINGER,A.A.STOOP,W.BODE,H.PANNEKOEK, JRNL AUTH 2 A.J.G.HORREVOETS JRNL TITL THE VARIABLE REGION-1 FROM TISSUE-TYPE PLASMINOGEN ACTIVATOR JRNL TITL 2 CONFERS SPECIFICITY FOR PLASMINOGEN ACTIVATOR INHIBITOR-1 TO JRNL TITL 3 THROMBIN BY FACILITATING CATALYSIS: RELEASE OF A KINETIC JRNL TITL 4 BLOCK BY A HETEROLOGOUS PROTEIN SURFACE LOOP JRNL REF J.MOL.BIOL. V. 293 613 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10543954 JRNL DOI 10.1006/JMBI.1999.3178 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 24228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2317 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.30 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.014 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.000 ; 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 1VR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-98. REMARK 100 THE DEPOSITION ID IS D_1000000257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 289 REMARK 200 PH : 7.6 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR 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 : 24804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 19.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 53.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 35.44000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.44000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.98000 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: L, H, I 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 ARG H 37A REMARK 465 ARG H 37B REMARK 465 SER H 37C REMARK 465 PRO H 37D REMARK 465 GLY H 37E REMARK 465 TRP H 147A REMARK 465 THR H 147B REMARK 465 ALA H 147C REMARK 465 ASN H 147D REMARK 465 VAL H 147E REMARK 465 GLY H 148 REMARK 465 LYS H 149 REMARK 465 GLN H 244 REMARK 465 PHE H 245 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 TYR H 184 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR H 184 OH REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS L 10 NZ REMARK 480 ARG L 14D CG CD NE CZ NH1 NH2 REMARK 480 ILE L 14K O CG1 CG2 CD1 REMARK 480 LEU H 33 CD1 CD2 REMARK 480 ARG H 50 CZ NH1 NH2 REMARK 480 ASP H 60E OD1 OD2 REMARK 480 GLU H 97A CG OE1 OE2 REMARK 480 LYS H 109 NZ REMARK 480 GLU H 127 CG REMARK 480 LYS H 145 CD CE NZ REMARK 480 GLN H 151 CB CG REMARK 480 PRO H 152 CD REMARK 480 ASP H 186A OD2 REMARK 480 LYS H 186D CD CE NZ REMARK 480 GLU H 217 CG REMARK 480 LYS H 236 CD CE NZ REMARK 480 GLN H 239 CG REMARK 480 LYS H 240 CG CD CE NZ REMARK 480 ASP H 243 C O REMARK 480 GLU I 61 C REMARK 480 GLU I 62 C 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 C ARG H 77A O HOH H 282 0.06 REMARK 500 CD GLU I 61 O HOH I 66 0.36 REMARK 500 CG GLU H 97A O HOH H 313 0.62 REMARK 500 CD1 LEU I 64 O HOH H 284 0.64 REMARK 500 S TYS I 63 O HOH I 65 0.88 REMARK 500 OE2 GLU I 61 O HOH I 66 1.02 REMARK 500 O2 TYS I 63 O HOH I 65 1.06 REMARK 500 O GLY H 219 O HOH H 315 1.12 REMARK 500 CD GLU H 97A O HOH H 313 1.19 REMARK 500 O ARG H 77A O HOH H 282 1.22 REMARK 500 OE1 GLU I 61 O HOH I 66 1.23 REMARK 500 O3 TYS I 63 O HOH I 65 1.38 REMARK 500 CB GLU H 97A O HOH H 313 1.39 REMARK 500 N ASN H 78 O HOH H 282 1.47 REMARK 500 CA ARG H 77A O HOH H 282 1.50 REMARK 500 OE1 GLU H 97A NH1 ARG H 175 1.78 REMARK 500 CG LEU I 64 O HOH H 284 1.82 REMARK 500 CG GLU I 61 O HOH I 66 1.85 REMARK 500 O1 TYS I 63 O HOH I 65 1.86 REMARK 500 OE2 GLU H 97A O HOH H 313 1.90 REMARK 500 OE1 GLU H 97A O HOH H 313 2.13 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 NH2 ARG H 75 O TYR H 76 2555 0.97 REMARK 500 NH2 ARG H 75 C TYR H 76 2555 1.47 REMARK 500 CG ARG H 75 NE ARG H 75 2555 1.99 REMARK 500 NH1 ARG H 75 OE1 GLU I 57 2555 2.01 REMARK 500 CD ARG H 75 O HOH I 67 2555 2.01 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 LYS L 10 CE LYS L 10 NZ -0.218 REMARK 500 ILE L 14K CB ILE L 14K CG2 -0.303 REMARK 500 LEU H 33 CG LEU H 33 CD2 0.250 REMARK 500 ARG H 39 C PHE H 40 N 0.157 REMARK 500 ARG H 50 NE ARG H 50 CZ -0.235 REMARK 500 ARG H 50 CZ ARG H 50 NH1 0.355 REMARK 500 ARG H 50 CZ ARG H 50 NH2 0.443 REMARK 500 ASP H 60E CG ASP H 60E OD1 -0.202 REMARK 500 ASP H 60E CG ASP H 60E OD2 0.555 REMARK 500 LYS H 70 C HIS H 71 N -0.155 REMARK 500 THR H 74 C ARG H 75 N -0.228 REMARK 500 GLU H 97A CB GLU H 97A CG -0.698 REMARK 500 GLU H 97A CG GLU H 97A CD 0.281 REMARK 500 GLU H 97A CD GLU H 97A OE1 0.322 REMARK 500 GLU H 97A CD GLU H 97A OE2 -0.327 REMARK 500 LYS H 145 CG LYS H 145 CD 0.211 REMARK 500 GLU H 217 CG GLU H 217 CD 0.203 REMARK 500 TYS I 63 C LEU I 64 N -0.216 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 ARG L 14D CD - NE - CZ ANGL. DEV. = 10.4 DEGREES REMARK 500 ILE L 14K CA - CB - CG2 ANGL. DEV. = 20.0 DEGREES REMARK 500 LEU H 33 CB - CG - CD1 ANGL. DEV. = 24.2 DEGREES REMARK 500 LYS H 36 CA - C - N ANGL. DEV. = 20.2 DEGREES REMARK 500 LYS H 36 O - C - N ANGL. DEV. = -23.2 DEGREES REMARK 500 ARG H 39 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG H 39 CA - C - N ANGL. DEV. = -35.4 DEGREES REMARK 500 ASP H 49 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG H 50 CD - NE - CZ ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG H 50 NH1 - CZ - NH2 ANGL. DEV. = -34.9 DEGREES REMARK 500 ARG H 50 NE - CZ - NH1 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG H 50 NE - CZ - NH2 ANGL. DEV. = -13.1 DEGREES REMARK 500 ASP H 60E OD1 - CG - OD2 ANGL. DEV. = -23.4 DEGREES REMARK 500 ASP H 60E CB - CG - OD1 ANGL. DEV. = 34.6 DEGREES REMARK 500 ASP H 60E CB - CG - OD2 ANGL. DEV. = -19.7 DEGREES REMARK 500 GLU H 61 CA - CB - CG ANGL. DEV. = 14.7 DEGREES REMARK 500 ARG H 67 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 THR H 74 O - C - N ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG H 75 C - N - CA ANGL. DEV. = 22.6 DEGREES REMARK 500 ARG H 75 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG H 75 O - C - N ANGL. DEV. = -15.9 DEGREES REMARK 500 GLU H 77 C - N - CA ANGL. DEV. = -27.1 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG H 77A CA - C - N ANGL. DEV. = -24.4 DEGREES REMARK 500 ASN H 78 O - C - N ANGL. DEV. = -27.3 DEGREES REMARK 500 GLU H 80 N - CA - CB ANGL. DEV. = 12.2 DEGREES REMARK 500 GLU H 80 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG H 93 CD - NE - CZ ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG H 93 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 GLU H 97A CA - CB - CG ANGL. DEV. = 26.6 DEGREES REMARK 500 GLU H 97A CB - CG - CD ANGL. DEV. = 31.1 DEGREES REMARK 500 GLU H 97A CG - CD - OE1 ANGL. DEV. = -16.5 DEGREES REMARK 500 ASN H 98 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 ASN H 98 CA - CB - CG ANGL. DEV. = -13.4 DEGREES REMARK 500 ASN H 98 N - CA - C ANGL. DEV. = 19.3 DEGREES REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 LYS H 109 CD - CE - NZ ANGL. DEV. = 13.9 DEGREES REMARK 500 ASP H 116 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP H 125 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 GLN H 151 CG - CD - OE1 ANGL. DEV. = -18.3 DEGREES REMARK 500 ARG H 206 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 GLU H 217 CG - CD - OE2 ANGL. DEV. = -20.6 DEGREES REMARK 500 LYS H 236 CB - CG - CD ANGL. DEV. = 35.3 DEGREES REMARK 500 GLN H 239 CG - CD - NE2 ANGL. DEV. = -17.4 DEGREES REMARK 500 LYS H 240 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 ASP H 243 CB - CA - C ANGL. DEV. = 24.3 DEGREES REMARK 500 PHE I 56 C - N - CA ANGL. DEV. = 18.4 DEGREES REMARK 500 LEU I 64 C - N - CA ANGL. DEV. = 17.3 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 PHE L 7 -88.43 -124.43 REMARK 500 PHE H 40 108.41 -55.89 REMARK 500 ASN H 60G 85.38 -152.66 REMARK 500 HIS H 71 -67.19 -152.26 REMARK 500 ASN H 78 21.99 83.51 REMARK 500 ILE H 79 -79.41 -146.15 REMARK 500 GLU H 97A -62.02 -120.36 REMARK 500 TYR H 184 165.46 142.15 REMARK 500 PHE I 56 102.82 99.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS H 36 HIS H 37 -116.99 REMARK 500 TYS I 63 LEU I 64 148.94 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 H 50 0.25 SIDE CHAIN REMARK 500 ASP H 60E 0.08 SIDE CHAIN REMARK 500 GLU H 97A 0.12 SIDE CHAIN REMARK 500 GLU H 127 0.10 SIDE CHAIN REMARK 500 GLU H 217 0.19 SIDE CHAIN REMARK 500 GLN H 239 0.13 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 LYS H 36 -13.16 REMARK 500 ARG H 39 27.55 REMARK 500 LYS H 70 -10.19 REMARK 500 ARG H 75 11.69 REMARK 500 ARG H 77A 19.34 REMARK 500 ASN H 78 -34.04 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 I OF HIRUDIN DBREF 1VR1 L 1B 14K UNP P00734 THRB_HUMAN 334 360 DBREF 1VR1 H 16 245 UNP P00734 THRB_HUMAN 364 620 DBREF 1VR1 I 55 64 UNP P28504 HIR2_HIRME 55 64 SEQADV 1VR1 ALA H 35 UNP P00734 CONFLICT SEQADV 1VR1 LYS H 36 UNP P00734 CONFLICT SEQADV 1VR1 HIS H 37 UNP P00734 CONFLICT SEQADV 1VR1 ARG H 37B UNP P00734 LYS 384 CONFLICT SEQADV 1VR1 GLY H 37E UNP P00734 GLN 387 CONFLICT SEQADV 1VR1 ARG H 39 UNP P00734 CONFLICT SEQADV 1VR1 PHE H 40 UNP P00734 LEU 389 CONFLICT SEQADV 1VR1 TYR H 184 UNP P00734 GLY 552 CONFLICT SEQRES 1 L 27 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 L 27 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 L 27 ILE SEQRES 1 H 261 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 261 TRP GLN VAL MET LEU PHE ALA LYS HIS ARG ARG SER PRO SEQRES 3 H 261 GLY GLU ARG PHE LEU CYS GLY ALA SER LEU ILE SER ASP SEQRES 4 H 261 ARG TRP VAL LEU THR ALA ALA HIS CYS LEU LEU TYR PRO SEQRES 5 H 261 PRO TRP ASP LYS ASN PHE THR GLU ASN ASP LEU LEU VAL SEQRES 6 H 261 ARG ILE GLY LYS HIS SER ARG THR ARG TYR GLU ARG ASN SEQRES 7 H 261 ILE GLU LYS ILE SER MET LEU GLU LYS ILE TYR ILE HIS SEQRES 8 H 261 PRO ARG TYR ASN TRP ARG GLU ASN LEU ASP ARG ASP ILE SEQRES 9 H 261 ALA LEU MET LYS LEU LYS LYS PRO VAL ALA PHE SER ASP SEQRES 10 H 261 TYR ILE HIS PRO VAL CYS LEU PRO ASP ARG GLU THR ALA SEQRES 11 H 261 ALA SER LEU LEU GLN ALA GLY TYR LYS GLY ARG VAL THR SEQRES 12 H 261 GLY TRP GLY ASN LEU LYS GLU THR TRP THR ALA ASN VAL SEQRES 13 H 261 GLY LYS GLY GLN PRO SER VAL LEU GLN VAL VAL ASN LEU SEQRES 14 H 261 PRO ILE VAL GLU ARG PRO VAL CYS LYS ASP SER THR ARG SEQRES 15 H 261 ILE ARG ILE THR ASP ASN MET PHE CYS ALA TYR TYR LYS SEQRES 16 H 261 PRO ASP GLU GLY LYS ARG GLY ASP ALA CYS GLU GLY ASP SEQRES 17 H 261 SER GLY GLY PRO PHE VAL MET LYS SER PRO PHE ASN ASN SEQRES 18 H 261 ARG TRP TYR GLN MET GLY ILE VAL SER TRP GLY GLU GLY SEQRES 19 H 261 CYS ASP ARG ASP GLY LYS TYR GLY PHE TYR THR HIS VAL SEQRES 20 H 261 PHE ARG LEU LYS LYS TRP ILE GLN LYS VAL ILE ASP GLN SEQRES 21 H 261 PHE SEQRES 1 I 10 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU MODRES 1VR1 TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HETNAM TYS O-SULFO-L-TYROSINE FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 HOH *81(H2 O) HELIX 1 1 GLU L 8 LYS L 10 5 3 HELIX 2 2 GLU L 14C SER L 14I 1 7 HELIX 3 3 ALA H 56 CYS H 58 5 3 HELIX 4 4 PRO H 60B TRP H 60D 5 3 HELIX 5 5 GLU H 61 ASP H 63 5 3 HELIX 6 6 ARG H 126 LEU H 129C 1 7 HELIX 7 7 ARG H 165 SER H 171 1 7 HELIX 8 8 PRO H 186 GLU H 186B 5 3 HELIX 9 9 PHE H 232 VAL H 241 5 10 SHEET 1 A 4 LYS H 81 MET H 84 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 ALA H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 A 4 PHE H 40 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 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 TRP H 215 -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 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.33 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.35 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.35 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.70 LINK C GLU I 62 N TYS I 63 1555 1555 1.47 LINK C TYS I 63 N LEU I 64 1555 1555 1.12 SITE 1 AC1 16 LYS H 36 HIS H 37 GLU H 38 PHE H 40 SITE 2 AC1 16 LEU H 65 ARG H 73 THR H 74 ARG H 75 SITE 3 AC1 16 TYR H 76 LYS H 81 ILE H 82 HOH H 277 SITE 4 AC1 16 HOH H 284 HOH I 65 HOH I 66 HOH I 67 CRYST1 70.880 71.960 73.040 90.00 100.65 90.00 C 1 2 1 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 0.014108 0.000000 0.002653 0.00000 SCALE2 0.000000 0.013897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013931 0.00000