PDB Short entry for 3F6U HEADER HYDROLASE/HYDROLASE INHIBITOR 06-NOV-08 3F6U TITLE CRYSTAL STRUCTURE OF HUMAN ACTIVATED PROTEIN C (APC) COMPLEXED WITH TITLE 2 PPACK CAVEAT 3F6U THE NE2 HIS H - C3 0G6 AND OG SER H 195 - C2 0G7 BONDS ARE CAVEAT 2 3F6U OUTSIDE ACCEPTED RANGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN K-DEPENDENT PROTEIN C HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: UNP RESIDUES 212-451; COMPND 5 SYNONYM: AUTOPROTHROMBIN IIA, ANTICOAGULANT PROTEIN C, BLOOD COMPND 6 COAGULATION FACTOR XIV; COMPND 7 EC: 3.4.21.69; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: VITAMIN K-DEPENDENT PROTEIN C LIGHT CHAIN; COMPND 10 CHAIN: L; COMPND 11 FRAGMENT: UNP RESIDUES 91-188; COMPND 12 SYNONYM: AUTOPROTHROMBIN IIA, ANTICOAGULANT PROTEIN C, BLOOD COMPND 13 COAGULATION FACTOR XIV; COMPND 14 EC: 3.4.21.69 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_TAXID: 9606 KEYWDS BLOOD COAGULATION, SERINE PROTEASE, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.E.SCHMIDT,K.PADMANABHAN,M.C.UNDERWOOD,W.BODE,T.MATHER,S.P.BAJAJ REVDAT 8 13-MAR-24 3F6U 1 COMPND SOURCE REVDAT 7 06-SEP-23 3F6U 1 REMARK LINK REVDAT 6 25-APR-12 3F6U 1 REMARK REVDAT 5 26-OCT-11 3F6U 1 REMARK REVDAT 4 10-AUG-11 3F6U 1 REMARK REVDAT 3 13-JUL-11 3F6U 1 VERSN REVDAT 2 24-FEB-09 3F6U 1 VERSN REVDAT 1 25-NOV-08 3F6U 0 JRNL AUTH A.E.SCHMIDT,K.PADMANABHAN,M.C.UNDERWOOD,W.BODE,T.MATHER, JRNL AUTH 2 S.P.BAJAJ JRNL TITL THERMODYNAMIC LINKAGE BETWEEN THE S1 SITE, THE NA+ SITE, AND JRNL TITL 2 THE CA2+ SITE IN THE PROTEASE DOMAIN OF HUMAN ACTIVATED JRNL TITL 3 PROTEIN C (APC). JRNL REF J.BIOL.CHEM. V. 277 28987 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12029084 JRNL DOI 10.1074/JBC.M201892200 REMARK 0 REMARK 0 THIS ENTRY 3F6U REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 STRUCTURAL DATA R1AUTSF DETERMINED BY AUTHORS OF THE PDB ENTRY REMARK 0 1AUT: AUTHOR T.MATHER,V.OGANESSYAN,P.HOF,W.BODE,R.HUBER, REMARK 0 S.FOUNDLING,C.ESMON REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 1AUT REMARK 0 AUTH T.MATHER,V.OGANESSYAN,P.HOF,R.HUBER,S.FOUNDLING,C.ESMON, REMARK 0 AUTH 2 W.BODE REMARK 0 TITL THE 2.8 A CRYSTAL STRUCTURE OF GLA-DOMAINLESS ACTIVATED REMARK 0 TITL 2 PROTEIN C. REMARK 0 REF EMBO J. V. 15 6822 1996 REMARK 0 REFN ISSN 0261-4189 REMARK 0 PMID 9003757 REMARK 2 REMARK 2 RESOLUTION. 2.80 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 12292 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1236 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 718 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2639 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.344 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.214 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.741 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2561 ; 0.027 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3482 ; 2.567 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 315 ; 7.563 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;37.006 ;23.796 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 394 ;21.996 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;22.480 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.165 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1950 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1149 ; 0.273 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1663 ; 0.333 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 120 ; 0.155 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.402 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 36 ; 0.263 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.366 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1579 ; 1.205 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2519 ; 2.258 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1041 ; 3.255 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 963 ; 5.321 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3F6U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050219. REMARK 200 REMARK 200 AUTHOR USED THE SF DATA FROM ENTRY 1AUT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.53000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.61500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.61500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.53000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.80000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, 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 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 ASP H 60 REMARK 475 GLU H 60A REMARK 475 SER H 61 REMARK 475 LYS H 62 REMARK 475 LYS H 149 REMARK 475 GLU H 149A REMARK 475 ALA H 149B REMARK 475 LYS H 149C REMARK 475 ARG H 149D REMARK 475 ASN H 150 REMARK 475 ARG H 151 REMARK 475 ASP L 71 REMARK 475 GLY L 72 REMARK 475 ILE L 73 REMARK 475 GLY L 74 REMARK 475 SER L 75 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 H 37 CB CG CD CE NZ REMARK 480 LYS H 63 N CA CB CG CD CE NZ REMARK 480 ARG H 75 CG CD NE CZ NH1 NH2 REMARK 480 LYS H 96 CD CE NZ REMARK 480 GLU H 148 C O CB CG CD OE1 OE2 REMARK 480 MET H 175 CG SD CE REMARK 480 ARG H 243 CB CG CD NE CZ NH1 NH2 REMARK 480 ASP H 244 O REMARK 480 ILE L 70 CB CG1 CG2 CD1 REMARK 480 PHE L 76 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 ARG L 91 CB CG CD NE CZ NH1 NH2 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 O MET H 59 N ASP H 60 1.72 REMARK 500 OE2 GLU H 167 O HOH H 328 1.75 REMARK 500 O SER L 75 O HOH L 20 1.86 REMARK 500 CE MET H 21 NH1 ARG H 151 2.10 REMARK 500 O HOH H 6 O HOH L 148 2.19 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 H 20 CD LYS H 20 CE 0.162 REMARK 500 CYS H 58 CB CYS H 58 SG -0.142 REMARK 500 LYS H 63 CA LYS H 63 C -0.251 REMARK 500 ARG H 75 CB ARG H 75 CG -0.264 REMARK 500 GLU H 77 CG GLU H 77 CD 0.092 REMARK 500 GLU H 148 CA GLU H 148 CB 0.133 REMARK 500 GLU H 148 CA GLU H 148 C -0.206 REMARK 500 GLU H 178 CG GLU H 178 CD 0.112 REMARK 500 ARG H 243 CA ARG H 243 CB -0.228 REMARK 500 ILE L 70 CA ILE L 70 CB -0.167 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 LEU H 34 CB - CG - CD2 ANGL. DEV. = -12.0 DEGREES REMARK 500 MET H 59 O - C - N ANGL. DEV. = -36.3 DEGREES REMARK 500 LYS H 63 CA - C - O ANGL. DEV. = -28.2 DEGREES REMARK 500 LYS H 63 CA - C - N ANGL. DEV. = 17.0 DEGREES REMARK 500 LEU H 81 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 LEU H 81 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES REMARK 500 ASP H 125 CB - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 ASP H 125 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP H 125 CB - CG - OD2 ANGL. DEV. = -8.9 DEGREES REMARK 500 PHE H 153 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 PHE H 153 CB - CG - CD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 LEU H 181 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES REMARK 500 ASP H 186A CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP H 186A CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG H 233 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG H 233 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 PRO L 54 C - N - CA ANGL. DEV. = 10.6 DEGREES REMARK 500 ILE L 70 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 ILE L 70 O - C - N ANGL. DEV. = -22.6 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 PRO H 28 0.34 -66.90 REMARK 500 ALA H 44 -177.97 -172.42 REMARK 500 TYR H 71 -58.14 -139.99 REMARK 500 TRP H 79 33.52 -92.21 REMARK 500 HIS H 144 -167.67 -104.28 REMARK 500 GLU H 148 -175.02 -39.06 REMARK 500 LYS H 149 108.22 -40.72 REMARK 500 ARG H 149D -77.91 -80.57 REMARK 500 ASN H 150 42.71 -148.62 REMARK 500 THR H 152 -30.97 -178.52 REMARK 500 ILE H 242 -72.72 -88.86 REMARK 500 ARG H 243 58.05 -55.23 REMARK 500 PRO L 54 21.99 -70.70 REMARK 500 ILE L 70 96.87 -48.57 REMARK 500 ASP L 71 156.88 -38.07 REMARK 500 HIS L 107 -93.65 -118.28 REMARK 500 PRO L 122 124.55 -28.53 REMARK 500 ASP L 129 -38.83 -33.80 REMARK 500 LEU L 130 15.49 56.55 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 GLY H 186 ASP H 186A -145.71 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 MET H 59 -43.01 REMARK 500 LYS H 63 25.12 REMARK 500 ILE L 70 29.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR IS BOUND TO THE ACTIVE SITE OF THE ENZYME. THE REMARK 600 UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. REMARK 600 UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A REMARK 600 COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT REMARK 600 BOND TO NE2 OF HIS 57 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 CA H 246 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU H 70 OE1 REMARK 620 2 GLU H 70 OE2 43.2 REMARK 620 3 ARG H 75 O 130.5 141.8 REMARK 620 4 GLU H 80 OE1 105.6 107.0 109.9 REMARK 620 5 GLU H 80 OE2 79.5 112.6 99.0 49.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 245 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE H 184A O REMARK 620 2 ASP H 186A O 67.5 REMARK 620 3 HOH H 339 O 82.3 113.1 REMARK 620 N 1 2 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0G6 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0G6 H 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 246 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AUT RELATED DB: PDB REMARK 900 THE 2.8 A CRYSTAL STRUCTURE OF GLA-DOMAINLESS ACTIVATED PROTEIN C. REMARK 900 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET. DBREF 3F6U H 16 244 UNP P04070 PROC_HUMAN 212 451 DBREF 3F6U L 49 146 UNP P04070 PROC_HUMAN 91 188 SEQRES 1 H 240 LEU ILE ASP GLY LYS MET THR ARG ARG GLY ASP SER PRO SEQRES 2 H 240 TRP GLN VAL VAL LEU LEU ASP SER LYS LYS LYS LEU ALA SEQRES 3 H 240 CYS GLY ALA VAL LEU ILE HIS PRO SER TRP VAL LEU THR SEQRES 4 H 240 ALA ALA HIS CYS MET ASP GLU SER LYS LYS LEU LEU VAL SEQRES 5 H 240 ARG LEU GLY GLU TYR ASP LEU ARG ARG TRP GLU LYS TRP SEQRES 6 H 240 GLU LEU ASP LEU ASP ILE LYS GLU VAL PHE VAL HIS PRO SEQRES 7 H 240 ASN TYR SER LYS SER THR THR ASP ASN ASP ILE ALA LEU SEQRES 8 H 240 LEU HIS LEU ALA GLN PRO ALA THR LEU SER GLN THR ILE SEQRES 9 H 240 VAL PRO ILE CYS LEU PRO ASP SER GLY LEU ALA GLU ARG SEQRES 10 H 240 GLU LEU ASN GLN ALA GLY GLN GLU THR LEU VAL THR GLY SEQRES 11 H 240 TRP GLY TYR HIS SER SER ARG GLU LYS GLU ALA LYS ARG SEQRES 12 H 240 ASN ARG THR PHE VAL LEU ASN PHE ILE LYS ILE PRO VAL SEQRES 13 H 240 VAL PRO HIS ASN GLU CYS SER GLU VAL MET SER ASN MET SEQRES 14 H 240 VAL SER GLU ASN MET LEU CYS ALA GLY ILE LEU GLY ASP SEQRES 15 H 240 ARG GLN ASP ALA CYS GLU GLY ASP SER GLY GLY PRO MET SEQRES 16 H 240 VAL ALA SER PHE HIS GLY THR TRP PHE LEU VAL GLY LEU SEQRES 17 H 240 VAL SER TRP GLY GLU GLY CYS GLY LEU LEU HIS ASN TYR SEQRES 18 H 240 GLY VAL TYR THR LYS VAL SER ARG TYR LEU ASP TRP ILE SEQRES 19 H 240 HIS GLY HIS ILE ARG ASP SEQRES 1 L 98 GLN CYS LEU VAL LEU PRO LEU GLU HIS PRO CYS ALA SER SEQRES 2 L 98 LEU CYS CYS GLY HIS GLY THR CYS ILE ASP GLY ILE GLY SEQRES 3 L 98 SER PHE SER CYS ASP CYS ARG SER GLY TRP GLU GLY ARG SEQRES 4 L 98 PHE CYS GLN ARG GLU VAL SER PHE LEU ASN CYS SER LEU SEQRES 5 L 98 ASP ASN GLY GLY CYS THR HIS TYR CYS LEU GLU GLU VAL SEQRES 6 L 98 GLY TRP ARG ARG CYS SER CYS ALA PRO GLY TYR LYS LEU SEQRES 7 L 98 GLY ASP ASP LEU LEU GLN CYS HIS PRO ALA VAL LYS PHE SEQRES 8 L 98 PRO CYS GLY ARG PRO TRP LYS HET 0G6 H 1 30 HET NA H 245 1 HET CA H 246 1 HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETSYN 0G6 PPACK FORMUL 3 0G6 C21 H34 CL N6 O3 1+ FORMUL 4 NA NA 1+ FORMUL 5 CA CA 2+ FORMUL 6 HOH *147(H2 O) HELIX 1 1 ALA H 55 MET H 59 5 5 HELIX 2 2 ASP H 125 GLU H 129 1 8 HELIX 3 3 PRO H 164 MET H 172 1 9 HELIX 4 4 TYR H 234 ARG H 243 1 10 HELIX 5 5 LEU L 100 CYS L 105 5 6 SHEET 1 A 7 LYS H 20 MET H 21 0 SHEET 2 A 7 ASN H 156 PRO H 161 -1 O PHE H 157 N LYS H 20 SHEET 3 A 7 GLU H 135 GLY H 140 -1 N THR H 136 O ILE H 160 SHEET 4 A 7 PRO H 198 PHE H 203 -1 O VAL H 200 N LEU H 137 SHEET 5 A 7 THR H 206 TRP H 215 -1 O THR H 206 N PHE H 203 SHEET 6 A 7 GLY H 226 LYS H 230 -1 O VAL H 227 N TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 N LEU H 181 O TYR H 228 SHEET 1 B 7 GLN H 30 LEU H 34 0 SHEET 2 B 7 LEU H 40 HIS H 48 -1 O ALA H 44 N VAL H 31 SHEET 3 B 7 TRP H 51 THR H 54 -1 O TRP H 51 N ILE H 47 SHEET 4 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 B 7 LEU H 81 VAL H 90 -1 N GLU H 87 O HIS H 107 SHEET 6 B 7 LEU H 65 LEU H 68 -1 N LEU H 68 O LEU H 81 SHEET 7 B 7 GLN H 30 LEU H 34 -1 N LEU H 34 O LEU H 65 SHEET 1 C 2 GLY L 67 CYS L 69 0 SHEET 2 C 2 CYS L 78 CYS L 80 -1 O ASP L 79 N THR L 68 SHEET 1 D 2 TRP L 84 GLU L 85 0 SHEET 2 D 2 ARG L 91 GLU L 92 -1 O ARG L 91 N GLU L 85 SHEET 1 E 2 TYR L 108 GLU L 111 0 SHEET 2 E 2 ARG L 116 SER L 119 -1 O ARG L 117 N LEU L 110 SHEET 1 F 2 TYR L 124 LEU L 126 0 SHEET 2 F 2 CYS L 133 PRO L 135 -1 O HIS L 134 N LYS L 125 SSBOND 1 CYS H 42 CYS H 58 1555 1555 2.00 SSBOND 2 CYS H 122 CYS L 141 1555 1555 2.02 SSBOND 3 CYS H 168 CYS H 182 1555 1555 1.98 SSBOND 4 CYS H 191 CYS H 220 1555 1555 1.99 SSBOND 5 CYS L 50 CYS L 69 1555 1555 2.00 SSBOND 6 CYS L 59 CYS L 64 1555 1555 2.03 SSBOND 7 CYS L 63 CYS L 78 1555 1555 2.04 SSBOND 8 CYS L 80 CYS L 89 1555 1555 1.99 SSBOND 9 CYS L 98 CYS L 109 1555 1555 2.07 SSBOND 10 CYS L 105 CYS L 118 1555 1555 2.04 SSBOND 11 CYS L 120 CYS L 133 1555 1555 2.01 LINK C3 0G6 H 1 NE2 HIS H 57 1555 1555 1.99 LINK C2 0G6 H 1 OG SER H 195 1555 1555 1.88 LINK OE1 GLU H 70 CA CA H 246 1555 1555 2.95 LINK OE2 GLU H 70 CA CA H 246 1555 1555 2.96 LINK O ARG H 75 CA CA H 246 1555 1555 2.52 LINK OE1 GLU H 80 CA CA H 246 1555 1555 2.58 LINK OE2 GLU H 80 CA CA H 246 1555 1555 2.69 LINK O ILE H 184A NA NA H 245 1555 1555 2.58 LINK O ASP H 186A NA NA H 245 1555 1555 2.85 LINK NA NA H 245 O HOH H 339 1555 1555 2.01 SITE 1 AC1 14 HIS H 57 THR H 99 ASN H 174 ASP H 189 SITE 2 AC1 14 ALA H 190 CYS H 191 GLY H 193 ASP H 194 SITE 3 AC1 14 SER H 195 SER H 214 TRP H 215 GLY H 216 SITE 4 AC1 14 GLY H 219 HOH H 342 SITE 1 AC2 5 ILE H 184A ASP H 186A LEU H 221A ASN H 224 SITE 2 AC2 5 HOH H 339 SITE 1 AC3 4 GLU H 70 ASP H 72 ARG H 75 GLU H 80 CRYST1 57.060 89.600 101.230 90.00 90.00 90.00 P 21 21 21 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 0.017525 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009878 0.00000