PDB Short entry for 1C5O HEADER BLOOD CLOTTING/HYDROLASE INHIBITOR 22-DEC-99 1C5O TITLE STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB- TITLE 2 MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: LIGHT CHAIN; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 FRAGMENT: HEAVY CHAIN; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HIRUDIN; COMPND 13 CHAIN: I SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 11 ORGANISM_TAXID: 6421 KEYWDS SELECTIVE, S1 SITE INHIBITOR, STRUCTURE-BASED DRUG DESIGN, UROKINASE, KEYWDS 2 TRYPSIN, THROMBIN, BLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.A.KATZ,R.MACKMAN,C.LUONG,K.RADIKA,A.MARTELLI,P.A.SPRENGELER,J.WANG, AUTHOR 2 H.CHAN,L.WONG REVDAT 7 04-AUG-21 1C5O 1 COMPND REMARK HET FORMUL REVDAT 7 2 1 LINK ATOM REVDAT 6 04-OCT-17 1C5O 1 REMARK REVDAT 5 01-JUN-16 1C5O 1 SOURCE REVDAT 4 13-JUL-11 1C5O 1 VERSN REVDAT 3 24-FEB-09 1C5O 1 VERSN REVDAT 2 26-SEP-01 1C5O 3 ATOM CONECT REVDAT 1 22-DEC-00 1C5O 0 JRNL AUTH B.A.KATZ,R.MACKMAN,C.LUONG,K.RADIKA,A.MARTELLI, JRNL AUTH 2 P.A.SPRENGELER,J.WANG,H.CHAN,L.WONG JRNL TITL STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, JRNL TITL 2 S1-BINDING, SUBMICROMOLAR INHIBITOR OF UROKINASE-TYPE JRNL TITL 3 PLASMINOGEN ACTIVATOR. JRNL REF CHEM.BIOL. V. 7 299 2000 JRNL REFN ISSN 1074-5521 JRNL PMID 10779411 JRNL DOI 10.1016/S1074-5521(00)00104-6 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.800 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 51.0 REMARK 3 NUMBER OF REFLECTIONS : 14335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : X-PLOR REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1437 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 26.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 832 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE : 0.4160 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 96 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 : 2430 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 426 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 4.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.460 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: REMARK 3 BULK SOLVENT TERMS INCLUDED IN FOB FILE CREATED WITH STANDARD X- REMARK 3 PLOR SCRIPT. REMARK 3 REMARK 3 ARG_H126 WAS SIMULTANEOUSLY REFINED IN TWO CONFORMATIONS. REMARK 3 REMARK 3 NO DENSITY WAS OBSERVED FOR TRP148, THR149, ALA149A, ASN149B, REMARK 3 VAL149C, REMARK 3 GLY149D, AND LYS149E IN THE AUTOLYSIS LOOP, AND THESE RESIDUES ARE REMARK 3 NOT REMARK 3 INCLUDED IN THE MODEL. REMARK 3 REMARK 3 DISORDERED WATERS INCLUDE: REMARK 3 HOH379, HOH380, AND HOH381 WHICH ARE CLOSE TO ONE ANOTHER; REMARK 3 HOH381 IS ALSO CLOSE TO HOH711; REMARK 3 HOH395 WHICH IS IN A SPECIAL POSITION. REMARK 3 HOH396 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH434 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH457 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF; REMARK 3 (THE ABOVE WATERS HAVE STRONG REMARK 3 DENSITY AND THEIR REFINED OCCUPANCIES ARE SIGNIFICANTLY REMARK 3 GREATER THAN UNITY. THEY MAY REFLECT A DIFFERENT FEATURE REMARK 3 THAN DISORDERED WATERS); REMARK 3 HOH797 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH809 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF; REMARK 3 HOH627 WHICH IS CLOSE TO HOH809. REMARK 3 HIS_H57 IS MONOPROTONATED ON THE DELTA NITROGEN. REMARK 3 HIS_H91 AND HIS_H119 ARE MONOPROTONATED ON THE EPSILON NITROGEN REMARK 4 REMARK 4 1C5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000001368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 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 : MSC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX (MSC) REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 38.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 51.0 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 26.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER PLUS REMARK 200 REFINEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THROMBIN WAS PURCHASED FROM REMARK 280 HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. REMARK 280 THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., REMARK 280 1991). THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) REMARK 280 WAS INCUBATED WITH 1.0 MM ACETYL-HIRUDIN, 10 MM BENZAMIDINE FOR REMARK 280 1 HR AT 4 DEG C. GLYCEROL WAS REMOVED AND THE COMPLEX REMARK 280 CONCENTRATED WITH A CENTRICON 10 (AMICON) TO ABOUT 10 MG/ML AS REMARK 280 DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM REMARK 280 ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-BENZMAIDINE WERE REMARK 280 GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. REMARK 280 THE DROPS WERE MADE FROM 5 MICROLITERS OF COMPLEX AND 5 REMARK 280 MICROLITERS OF RESERVOIR SOLUTION (0.10 M TRIS, 0.50 M NACL, 22 % REMARK 280 (BY VOLUME) PEG 4K, PH 7.5)., VAPOR DIFFUSION 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 35.73000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.91000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.73000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.91000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH H 742 LIES ON A SPECIAL POSITION. 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 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 147F REMARK 465 LYS H 147G REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 PHE L 1G 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 GLU L 1C N CA C O REMARK 480 GLY H 246 C O REMARK 480 GLU I 61 CB CG CD OE1 OE2 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 H2 HOH L 381 O HOH L 711 1.39 REMARK 500 O LEU H 64 H2 HOH H 465 1.46 REMARK 500 O VAL H 163 H1 HOH H 446 1.48 REMARK 500 O VAL H 121 H2 HOH H 466 1.49 REMARK 500 O ILE H 16 H2 HOH H 473 1.52 REMARK 500 O HOH H 703 H2 HOH H 771 1.54 REMARK 500 O GLY H 133 H1 HOH H 512 1.54 REMARK 500 O THR H 139 H1 HOH H 432 1.55 REMARK 500 O GLU H 23 H1 HOH H 450 1.55 REMARK 500 O ILE H 162 H2 HOH H 449 1.56 REMARK 500 H1 HOH H 623 O HOH H 747 1.57 REMARK 500 O SER H 115 H1 HOH H 452 1.58 REMARK 500 O LYS H 186D H2 HOH H 459 1.58 REMARK 500 O LEU L 6 H2 HOH L 449 1.59 REMARK 500 H2 HOH L 473 O HOH L 522 1.59 REMARK 500 O ARG H 77A H1 HOH H 425 1.59 REMARK 500 O LEU H 144 H2 HOH H 500 1.60 REMARK 500 O HOH L 381 O HOH L 711 2.04 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 H1 HOH H 425 H2 HOH H 425 2555 0.39 REMARK 500 H1 HOH H 426 H1 HOH H 426 2555 0.45 REMARK 500 O HOH H 425 O HOH H 425 2555 0.72 REMARK 500 O HOH H 425 H2 HOH H 425 2555 0.74 REMARK 500 H2 HOH H 462 H2 HOH H 462 2555 0.80 REMARK 500 O HOH H 426 H1 HOH H 426 2555 1.22 REMARK 500 H1 HOH H 426 H2 HOH H 462 2555 1.23 REMARK 500 H2 HOH H 425 H2 HOH H 425 2555 1.31 REMARK 500 O HOH H 681 H2 HOH H 773 2555 1.49 REMARK 500 O HOH H 425 H1 HOH H 425 2555 1.50 REMARK 500 O HOH L 381 O HOH L 381 2556 2.00 REMARK 500 O HOH L 381 O HOH L 707 2556 2.11 REMARK 500 O HOH H 426 O HOH H 426 2555 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS H 57 CG HIS H 57 ND1 -0.101 REMARK 500 HIS H 91 NE2 HIS H 91 CD2 -0.084 REMARK 500 HIS H 230 CG HIS H 230 ND1 -0.097 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 L 1D N - CA - C ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG L 4 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TYR L 14J N - CA - C ANGL. DEV. = -17.8 DEGREES REMARK 500 TRP H 29 CG - CD1 - NE1 ANGL. DEV. = -8.4 DEGREES REMARK 500 TRP H 29 CD1 - NE1 - CE2 ANGL. DEV. = 9.4 DEGREES REMARK 500 TRP H 29 NE1 - CE2 - CZ2 ANGL. DEV. = 9.6 DEGREES REMARK 500 TRP H 29 NE1 - CE2 - CD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TRP H 51 CD1 - NE1 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 TRP H 51 NE1 - CE2 - CZ2 ANGL. DEV. = 8.2 DEGREES REMARK 500 TRP H 51 NE1 - CE2 - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP H 60D CG - CD1 - NE1 ANGL. DEV. = -6.6 DEGREES REMARK 500 TRP H 60D CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 TRP H 60D NE1 - CE2 - CZ2 ANGL. DEV. = 7.7 DEGREES REMARK 500 TRP H 60D NE1 - CE2 - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP H 63 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG H 73 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 TRP H 96 CG - CD1 - NE1 ANGL. DEV. = -6.9 DEGREES REMARK 500 TRP H 96 CD1 - NE1 - CE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 TRP H 96 NE1 - CE2 - CZ2 ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 TRP H 141 CG - CD1 - NE1 ANGL. DEV. = -8.1 DEGREES REMARK 500 TRP H 141 CD1 - NE1 - CE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 TRP H 141 NE1 - CE2 - CZ2 ANGL. DEV. = 9.7 DEGREES REMARK 500 CYS H 182 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP H 186A CB - CG - OD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 ARG H 187 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 PHE H 199 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 ARG H 206 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP H 207 CG - CD1 - NE1 ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP H 207 CD1 - NE1 - CE2 ANGL. DEV. = 8.4 DEGREES REMARK 500 TRP H 207 NE1 - CE2 - CZ2 ANGL. DEV. = 6.9 DEGREES REMARK 500 TRP H 207 NE1 - CE2 - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP H 215 CG - CD1 - NE1 ANGL. DEV. = -6.9 DEGREES REMARK 500 TRP H 215 CD1 - NE1 - CE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 TRP H 215 NE1 - CE2 - CZ2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG H 233 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 TRP H 237 CG - CD1 - NE1 ANGL. DEV. = -7.1 DEGREES REMARK 500 TRP H 237 CD1 - NE1 - CE2 ANGL. DEV. = 7.8 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 1G -150.99 -125.08 REMARK 500 ALA L 1B -55.11 159.94 REMARK 500 PHE L 7 -77.92 -133.27 REMARK 500 TYR L 14J 60.67 -112.11 REMARK 500 ILE L 14K 37.82 37.15 REMARK 500 ASP L 14L 142.23 76.09 REMARK 500 LYS H 36 -70.85 -86.06 REMARK 500 LEU H 41 -57.53 -120.17 REMARK 500 ASN H 60G 86.78 -167.79 REMARK 500 ASN H 62 -14.70 -47.48 REMARK 500 HIS H 71 -57.04 -143.92 REMARK 500 PRO H 92 -9.44 -55.48 REMARK 500 GLU H 97A -71.83 -106.25 REMARK 500 SER H 115 -143.03 -150.43 REMARK 500 GLU H 186B 24.07 -76.16 REMARK 500 ARG H 187 -164.23 -121.78 REMARK 500 ASP H 189 175.72 172.99 REMARK 500 ASN H 205 29.87 37.84 REMARK 500 VAL H 231 -55.94 -29.24 REMARK 500 GLU I 61 -32.18 -38.04 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 L 15 0.12 SIDE CHAIN REMARK 500 ARG H 50 0.12 SIDE CHAIN REMARK 500 ARG H 97 0.16 SIDE CHAIN REMARK 500 ARG H 175 0.09 SIDE CHAIN REMARK 500 ARG H 187 0.15 SIDE CHAIN REMARK 500 ARG H 233 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 409 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 100.8 REMARK 620 3 HOH H 444 O 166.2 72.0 REMARK 620 4 HOH H 447 O 86.9 87.6 81.2 REMARK 620 5 HOH H 469 O 93.8 165.0 93.0 90.2 REMARK 620 6 HOH H 471 O 91.5 84.4 99.3 171.4 98.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN H 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN DBREF 1C5O L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1C5O H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1C5O I 55 65 UNP P28504 HIR2_HIRME 55 65 SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 I 11 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 1C5O TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 24 HET NA H 409 1 HET BEN H 410 18 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM BEN BENZAMIDINE FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA NA 1+ FORMUL 5 BEN C7 H8 N2 FORMUL 6 HOH *426(H2 O) HELIX 1 1 PHE L 7 SER L 11 5 5 HELIX 2 3 ALA H 55 CYS H 58 5 4 HELIX 3 6 ASP H 125 LEU H 130 1 9 HELIX 4 7 GLU H 164 ASP H 170 1 7 HELIX 5 9 LEU H 234 GLY H 246 1 13 SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139 SHEET 5 A 7 TRP H 207 TRP H 215 -1 N TYR H 208 O MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 N PHE H 227 O TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228 SHEET 1 B 7 LYS H 81 SER H 83 0 SHEET 2 B 7 LEU H 64 ILE H 68 -1 O VAL H 66 N SER H 83 SHEET 3 B 7 GLN H 30 ARG H 35 -1 O MET H 32 N ARG H 67 SHEET 4 B 7 LEU H 40 LEU H 46 -1 N LEU H 41 O LEU H 33 SHEET 5 B 7 TRP H 51 THR H 54 -1 N LEU H 53 O SER H 45 SHEET 6 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 B 7 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 1 C 2 LEU H 60 TYR H 60A 0 SHEET 2 C 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.02 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.01 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.01 LINK C GLU I 62 N TYS I 63 1555 1555 1.30 LINK C TYS I 63 N LEU I 64 1555 1555 1.30 LINK O ARG H 221A NA NA H 409 1555 1555 2.38 LINK O LYS H 224 NA NA H 409 1555 1555 2.49 LINK NA NA H 409 O HOH H 444 1555 1555 2.62 LINK NA NA H 409 O HOH H 447 1555 1555 2.69 LINK NA NA H 409 O HOH H 469 1555 1555 2.69 LINK NA NA H 409 O HOH H 471 1555 1555 2.72 CISPEP 1 SER H 36A PRO H 37 0 -27.15 SITE 1 AC1 6 ARG H 221A LYS H 224 HOH H 444 HOH H 447 SITE 2 AC1 6 HOH H 469 HOH H 471 SITE 1 AC2 6 ASP H 189 ALA H 190 SER H 195 VAL H 213 SITE 2 AC2 6 GLY H 219 HOH H 600 SITE 1 AC3 16 PHE H 34 LYS H 36 LEU H 40 LEU H 65 SITE 2 AC3 16 ARG H 73 THR H 74 ARG H 75 TYR H 76 SITE 3 AC3 16 LYS H 81 ILE H 82 MET H 84 HOH H 490 SITE 4 AC3 16 HOH I 499 HOH I 520 HOH I 535 HOH I 597 CRYST1 71.460 71.820 72.850 90.00 100.90 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 0.013994 0.000000 0.002695 0.00000 SCALE2 0.000000 0.013924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013979 0.00000