HEADER HYDROLASE/HYDROLASE INHIBITOR/RNA 02-MAY-17 5VOF TITLE DESGLA-XAS195A BOUND TO APTAMER 11F7T AND RIVAROXABAN CAVEAT 5VOF COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR X; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: RESIDUE 235-467; COMPND 5 SYNONYM: STUART FACTOR,STUART-PROWER FACTOR; COMPND 6 EC: 3.4.21.6; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: COAGULATION FACTOR X; COMPND 11 CHAIN: L; COMPND 12 FRAGMENT: RESIDUES 128-178; COMPND 13 SYNONYM: STUART FACTOR,STUART-PROWER FACTOR; COMPND 14 EC: 3.4.21.6; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: DNA/RNA (36-MER); COMPND 18 CHAIN: A; COMPND 19 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: F10; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: F10; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS SERINE PROTEASE, BLOOD COAGULATION, APTAMER, INHIBITOR, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.KRISHNASWAMY,S.KUMAR REVDAT 4 04-OCT-23 5VOF 1 LINK REVDAT 3 04-DEC-19 5VOF 1 LINK REVDAT 2 19-DEC-18 5VOF 1 JRNL REVDAT 1 13-JUN-18 5VOF 0 JRNL AUTH R.GUNARATNE,S.KUMAR,J.W.FREDERIKSEN,S.STAYROOK,J.L.LOHRMANN, JRNL AUTH 2 K.PERRY,K.M.BOMPIANI,C.V.CHABATA,N.K.THALJI,M.D.HO, JRNL AUTH 3 G.AREPALLY,R.M.CAMIRE,S.KRISHNASWAMY,B.A.SULLENGER JRNL TITL COMBINATION OF APTAMER AND DRUG FOR REVERSIBLE JRNL TITL 2 ANTICOAGULATION IN CARDIOPULMONARY BYPASS. JRNL REF NAT. BIOTECHNOL. V. 36 606 2018 JRNL REFN ISSN 1546-1696 JRNL PMID 29863725 JRNL DOI 10.1038/NBT.4153 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 25278 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1756 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2206 REMARK 3 NUCLEIC ACID ATOMS : 760 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.77000 REMARK 3 B22 (A**2) : 0.42000 REMARK 3 B33 (A**2) : 0.35000 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): 0.250 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.181 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.313 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3137 ; 0.008 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2414 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4339 ; 1.903 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5629 ; 0.987 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.471 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;31.421 ;24.299 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 388 ;13.125 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.038 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 472 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2965 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 659 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1124 ; 1.252 ; 2.539 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1123 ; 1.253 ; 2.538 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1398 ; 1.996 ; 3.804 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1399 ; 1.996 ; 3.805 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2013 ; 1.508 ; 2.718 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2014 ; 1.508 ; 2.719 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2942 ; 2.336 ; 4.055 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3641 ; 5.690 ;29.053 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3628 ; 5.682 ;28.906 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 16 H 243 REMARK 3 ORIGIN FOR THE GROUP (A): -12.7480 -27.0680 -8.8630 REMARK 3 T TENSOR REMARK 3 T11: 0.0921 T22: 0.0598 REMARK 3 T33: 0.2495 T12: 0.0510 REMARK 3 T13: 0.0540 T23: 0.0235 REMARK 3 L TENSOR REMARK 3 L11: 2.1662 L22: 4.1673 REMARK 3 L33: 1.4332 L12: 0.0536 REMARK 3 L13: 0.2885 L23: -0.5447 REMARK 3 S TENSOR REMARK 3 S11: 0.1086 S12: 0.1709 S13: -0.1148 REMARK 3 S21: -0.4532 S22: -0.1821 S23: -0.2871 REMARK 3 S31: 0.0373 S32: 0.2016 S33: 0.0736 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 88 L 138 REMARK 3 ORIGIN FOR THE GROUP (A): -35.7480 -31.6200 -3.7840 REMARK 3 T TENSOR REMARK 3 T11: 0.0781 T22: 0.1062 REMARK 3 T33: 0.3612 T12: 0.0388 REMARK 3 T13: -0.0610 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 6.2796 L22: 2.8302 REMARK 3 L33: 4.6112 L12: -0.3036 REMARK 3 L13: -2.6897 L23: -0.3441 REMARK 3 S TENSOR REMARK 3 S11: 0.3746 S12: 0.5021 S13: 0.1160 REMARK 3 S21: -0.1647 S22: -0.1616 S23: 0.3781 REMARK 3 S31: -0.2407 S32: -0.6273 S33: -0.2129 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 36 REMARK 3 ORIGIN FOR THE GROUP (A): -17.6120 -4.5520 -23.0230 REMARK 3 T TENSOR REMARK 3 T11: 0.8308 T22: 0.5185 REMARK 3 T33: 0.4075 T12: 0.3329 REMARK 3 T13: 0.0105 T23: 0.0542 REMARK 3 L TENSOR REMARK 3 L11: 1.2685 L22: 4.4818 REMARK 3 L33: 1.6353 L12: 1.5069 REMARK 3 L13: 0.8681 L23: 1.1469 REMARK 3 S TENSOR REMARK 3 S11: -0.1454 S12: 0.1467 S13: 0.3614 REMARK 3 S21: -1.2620 S22: -0.2306 S23: 0.2537 REMARK 3 S31: -0.5402 S32: -0.2533 S33: 0.3760 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VOF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : RIGAKU MICROMAX-007 HF 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27265 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 37.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.61900 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: REFMAC REMARK 200 STARTING MODEL: 2Y5G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE, 0.1 M TRIS BASE, 0.1 M REMARK 280 CARBOXYLIC ACIDS, 10% PEG 20,000, 20% PEG 500 MME, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 62.26050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.26050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.87200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 82.13750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.87200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 82.13750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 62.26050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.87200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 82.13750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 62.26050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.87200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 82.13750 REMARK 290 SMTRY3 8 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: H, L, A 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 LYS H 148 REMARK 465 GLY H 149 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 OP2 A A 10 MG MG A 102 1.50 REMARK 500 O1P CFL A 22 MG MG A 101 1.67 REMARK 500 CG ARG H 143 O ARG H 150 1.69 REMARK 500 SG CYS H 191 SG CYS H 220 1.78 REMARK 500 C GLU H 146 NH1 ARG H 150 1.83 REMARK 500 N2 G A 3 O2 CFL A 34 1.97 REMARK 500 OP2 G A 5 O HOH A 201 2.17 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 A A 4 O3' G A 5 P -0.092 REMARK 500 CFL A 6 O3' CFL A 7 P -0.699 REMARK 500 A A 10 O3' G A 11 P -0.095 REMARK 500 CFL A 12 O3' G A 13 P 0.092 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 CYS H 220 CA - CB - SG ANGL. DEV. = 9.9 DEGREES REMARK 500 A A 4 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 G A 5 C3' - O3' - P ANGL. DEV. = -15.4 DEGREES REMARK 500 CFL A 6 C3' - O3' - P ANGL. DEV. = 21.2 DEGREES REMARK 500 CFL A 7 O3' - P - O5' ANGL. DEV. = -18.0 DEGREES REMARK 500 CFL A 9 O3' - P - O5' ANGL. DEV. = -17.8 DEGREES REMARK 500 A A 10 O3' - P - OP2 ANGL. DEV. = 17.4 DEGREES REMARK 500 A A 10 O3' - P - OP1 ANGL. DEV. = -22.2 DEGREES REMARK 500 CFL A 12 C3' - O3' - P ANGL. DEV. = -23.1 DEGREES REMARK 500 G A 13 O3' - P - OP2 ANGL. DEV. = 32.9 DEGREES REMARK 500 G A 13 O3' - P - OP1 ANGL. DEV. = -34.6 DEGREES REMARK 500 A A 19 C3' - O3' - P ANGL. DEV. = 12.6 DEGREES REMARK 500 UFT A 20 O3' - P - O5' ANGL. DEV. = 14.2 DEGREES REMARK 500 CFL A 22 O3' - P - O5' ANGL. DEV. = -18.9 DEGREES REMARK 500 CFL A 22 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 UFT A 23 O3' - P - O5' ANGL. DEV. = -13.5 DEGREES REMARK 500 UFT A 23 O3' - P - OP2 ANGL. DEV. = 9.7 DEGREES REMARK 500 CFL A 27 O3' - P - O5' ANGL. DEV. = -12.4 DEGREES REMARK 500 CFL A 27 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 CFL A 30 C3' - O3' - P ANGL. DEV. = 19.3 DEGREES REMARK 500 CFL A 32 O3' - P - O5' ANGL. DEV. = -14.3 DEGREES REMARK 500 UFT A 33 O3' - P - OP2 ANGL. DEV. = 8.1 DEGREES REMARK 500 UFT A 33 C3' - O3' - P ANGL. DEV. = 12.9 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 ARG H 71 -35.32 -133.20 REMARK 500 GLN L 98 -112.68 -128.11 REMARK 500 LYS L 122 -48.26 -136.36 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 CA H 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP H 70 OD1 REMARK 620 2 ASN H 72 O 87.4 REMARK 620 3 GLN H 75 O 164.4 77.1 REMARK 620 4 GLU H 76 OE2 74.9 86.9 101.8 REMARK 620 5 GLU H 80 OE2 102.7 165.2 92.2 85.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR H 185 O REMARK 620 2 ASP H 185A O 72.2 REMARK 620 3 ARG H 222 O 146.5 79.2 REMARK 620 4 LYS H 224 O 84.6 99.3 83.0 REMARK 620 5 HOH H 419 O 105.4 171.3 100.2 72.1 REMARK 620 6 HOH H 421 O 101.4 79.8 90.2 173.1 108.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 10 OP1 REMARK 620 2 UFT A 23 OP2 159.5 REMARK 620 3 HOH A 202 O 106.2 67.6 REMARK 620 4 HOH A 203 O 77.2 108.2 175.5 REMARK 620 5 HOH A 207 O 80.7 79.9 90.7 86.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 UFT A 24 O4 REMARK 620 2 HOH A 208 O 163.4 REMARK 620 3 HOH A 212 O 88.6 81.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RIV H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 102 DBREF 5VOF H 16 243 UNP P00742 FA10_HUMAN 235 467 DBREF 5VOF L 88 138 UNP P00742 FA10_HUMAN 128 178 DBREF 5VOF A 1 36 PDB 5VOF 5VOF 1 36 SEQADV 5VOF ALA H 195 UNP P00742 SER 419 ENGINEERED MUTATION SEQRES 1 H 233 ILE VAL GLY GLY GLN GLU CYS LYS ASP GLY GLU CYS PRO SEQRES 2 H 233 TRP GLN ALA LEU LEU ILE ASN GLU GLU ASN GLU GLY PHE SEQRES 3 H 233 CYS GLY GLY THR ILE LEU SER GLU PHE TYR ILE LEU THR SEQRES 4 H 233 ALA ALA HIS CYS LEU TYR GLN ALA LYS ARG PHE LYS VAL SEQRES 5 H 233 ARG VAL GLY ASP ARG ASN THR GLU GLN GLU GLU GLY GLY SEQRES 6 H 233 GLU ALA VAL HIS GLU VAL GLU VAL VAL ILE LYS HIS ASN SEQRES 7 H 233 ARG PHE THR LYS GLU THR TYR ASP PHE ASP ILE ALA VAL SEQRES 8 H 233 LEU ARG LEU LYS THR PRO ILE THR PHE ARG MET ASN VAL SEQRES 9 H 233 ALA PRO ALA CYS LEU PRO GLU ARG ASP TRP ALA GLU SER SEQRES 10 H 233 THR LEU MET THR GLN LYS THR GLY ILE VAL SER GLY PHE SEQRES 11 H 233 GLY ARG THR HIS GLU LYS GLY ARG GLN SER THR ARG LEU SEQRES 12 H 233 LYS MET LEU GLU VAL PRO TYR VAL ASP ARG ASN SER CYS SEQRES 13 H 233 LYS LEU SER SER SER PHE ILE ILE THR GLN ASN MET PHE SEQRES 14 H 233 CYS ALA GLY TYR ASP THR LYS GLN GLU ASP ALA CYS GLN SEQRES 15 H 233 GLY ASP ALA GLY GLY PRO HIS VAL THR ARG PHE LYS ASP SEQRES 16 H 233 THR TYR PHE VAL THR GLY ILE VAL SER TRP GLY GLU GLY SEQRES 17 H 233 CYS ALA ARG LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 H 233 THR ALA PHE LEU LYS TRP ILE ASP ARG SER MET LYS SEQRES 1 L 51 LEU CYS SER LEU ASP ASN GLY ASP CYS ASP GLN PHE CYS SEQRES 2 L 51 HIS GLU GLU GLN ASN SER VAL VAL CYS SER CYS ALA ARG SEQRES 3 L 51 GLY TYR THR LEU ALA ASP ASN GLY LYS ALA CYS ILE PRO SEQRES 4 L 51 THR GLY PRO TYR PRO CYS GLY LYS GLN THR LEU GLU SEQRES 1 A 36 G A G A G CFL CFL CFL CFL A G CFL G SEQRES 2 A 36 A G A UFT A A UFT A CFL UFT UFT G G SEQRES 3 A 36 CFL CFL CFL CFL G CFL UFT CFL UFT UFT HET CFL A 6 20 HET CFL A 7 20 HET CFL A 8 20 HET CFL A 9 20 HET CFL A 12 20 HET UFT A 17 20 HET UFT A 20 20 HET CFL A 22 20 HET UFT A 23 20 HET UFT A 24 20 HET CFL A 27 20 HET CFL A 28 20 HET CFL A 29 20 HET CFL A 30 20 HET CFL A 32 20 HET UFT A 33 20 HET CFL A 34 20 HET UFT A 35 20 HET UFT A 36 20 HET RIV H 301 29 HET NA H 302 1 HET CA H 303 1 HET MG A 101 1 HET MG A 102 1 HETNAM CFL 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 CFL ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE HETNAM UFT 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM RIV 5-CHLORO-N-({(5S)-2-OXO-3-[4-(3-OXOMORPHOLIN-4-YL) HETNAM 2 RIV PHENYL]-1,3-OXAZOLIDIN-5-YL}METHYL)THIOPHENE-2- HETNAM 3 RIV CARBOXAMIDE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM MG MAGNESIUM ION HETSYN CFL 2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETSYN RIV RIVAROXABAN FORMUL 3 CFL 12(C9 H13 F N3 O7 P) FORMUL 3 UFT 7(C9 H12 F N2 O8 P) FORMUL 4 RIV C19 H18 CL N3 O5 S FORMUL 5 NA NA 1+ FORMUL 6 CA CA 2+ FORMUL 7 MG 2(MG 2+) FORMUL 9 HOH *93(H2 O) HELIX 1 AA1 ALA H 56 GLN H 61 5 6 HELIX 2 AA2 GLU H 124A LEU H 131A 1 9 HELIX 3 AA3 ASP H 164 SER H 172 1 9 HELIX 4 AA4 PHE H 234 MET H 242 1 9 HELIX 5 AA5 LEU L 91 CYS L 96 5 6 SHEET 1 AA1 8 GLN H 20 GLU H 21 0 SHEET 2 AA1 8 LYS H 156 VAL H 163 -1 O MET H 157 N GLN H 20 SHEET 3 AA1 8 MET H 180 ALA H 183 -1 O CYS H 182 N VAL H 163 SHEET 4 AA1 8 GLY H 226 LYS H 230 -1 O TYR H 228 N PHE H 181 SHEET 5 AA1 8 THR H 206 TRP H 215 -1 N TRP H 215 O ILE H 227 SHEET 6 AA1 8 PRO H 198 PHE H 203 -1 N THR H 201 O PHE H 208 SHEET 7 AA1 8 THR H 135 GLY H 140 -1 N ILE H 137 O VAL H 200 SHEET 8 AA1 8 LYS H 156 VAL H 163 -1 O LEU H 158 N VAL H 138 SHEET 1 AA2 7 ALA H 81 HIS H 83 0 SHEET 2 AA2 7 LYS H 65 VAL H 68 -1 N VAL H 66 O HIS H 83 SHEET 3 AA2 7 GLN H 30 ILE H 34 -1 N LEU H 32 O ARG H 67 SHEET 4 AA2 7 GLY H 40 ILE H 46 -1 O CYS H 42 N LEU H 33 SHEET 5 AA2 7 TYR H 51 THR H 54 -1 O LEU H 53 N THR H 45 SHEET 6 AA2 7 ALA H 104 LEU H 108 -1 O LEU H 106 N ILE H 52 SHEET 7 AA2 7 VAL H 85 LYS H 90 -1 N ILE H 89 O VAL H 105 SHEET 1 AA3 2 PHE L 99 GLU L 103 0 SHEET 2 AA3 2 SER L 106 SER L 110 -1 O SER L 106 N GLU L 103 SHEET 1 AA4 2 TYR L 115 LEU L 117 0 SHEET 2 AA4 2 CYS L 124 PRO L 126 -1 O ILE L 125 N THR L 116 SSBOND 1 CYS H 22 CYS H 27 1555 1555 2.05 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.06 SSBOND 3 CYS H 122 CYS L 132 1555 1555 2.06 SSBOND 4 CYS H 168 CYS H 182 1555 1555 2.00 SSBOND 5 CYS L 89 CYS L 100 1555 1555 2.08 SSBOND 6 CYS L 96 CYS L 109 1555 1555 2.05 SSBOND 7 CYS L 111 CYS L 124 1555 1555 2.06 LINK O3' G A 5 P CFL A 6 1555 1555 1.55 LINK O3' CFL A 6 P CFL A 7 1555 1555 0.91 LINK O3' CFL A 7 P CFL A 8 1555 1555 1.61 LINK O3' CFL A 8 P CFL A 9 1555 1555 1.61 LINK O3' CFL A 9 P A A 10 1555 1555 1.59 LINK O3' G A 11 P CFL A 12 1555 1555 1.60 LINK O3' CFL A 12 P G A 13 1555 1555 1.70 LINK O3' A A 16 P UFT A 17 1555 1555 1.60 LINK O3' UFT A 17 P A A 18 1555 1555 1.59 LINK O3' A A 19 P UFT A 20 1555 1555 1.58 LINK O3' UFT A 20 P A A 21 1555 1555 1.57 LINK O3' A A 21 P CFL A 22 1555 1555 1.58 LINK O3' CFL A 22 P UFT A 23 1555 1555 1.60 LINK O3' UFT A 23 P UFT A 24 1555 1555 1.60 LINK O3' UFT A 24 P G A 25 1555 1555 1.62 LINK O3' G A 26 P CFL A 27 1555 1555 1.61 LINK O3' CFL A 27 P CFL A 28 1555 1555 1.62 LINK O3' CFL A 28 P CFL A 29 1555 1555 1.61 LINK O3' CFL A 29 P CFL A 30 1555 1555 1.61 LINK O3' CFL A 30 P G A 31 1555 1555 1.59 LINK O3' G A 31 P CFL A 32 1555 1555 1.60 LINK O3' CFL A 32 P UFT A 33 1555 1555 1.57 LINK O3' UFT A 33 P CFL A 34 1555 1555 1.58 LINK O3' CFL A 34 P UFT A 35 1555 1555 1.60 LINK O3' UFT A 35 P UFT A 36 1555 1555 1.61 LINK OD1 ASP H 70 CA CA H 303 1555 1555 2.41 LINK O ASN H 72 CA CA H 303 1555 1555 2.31 LINK O GLN H 75 CA CA H 303 1555 1555 2.88 LINK OE2 GLU H 76 CA CA H 303 1555 1555 3.13 LINK OE2 GLU H 80 CA CA H 303 1555 1555 2.32 LINK O TYR H 185 NA NA H 302 1555 1555 2.35 LINK O ASP H 185A NA NA H 302 1555 1555 2.75 LINK O ARG H 222 NA NA H 302 1555 1555 2.52 LINK O LYS H 224 NA NA H 302 1555 1555 2.46 LINK NA NA H 302 O HOH H 419 1555 1555 2.55 LINK NA NA H 302 O HOH H 421 1555 1555 2.40 LINK OP1 A A 10 MG MG A 101 1555 1555 2.78 LINK OP2 UFT A 23 MG MG A 101 1555 1555 2.17 LINK O4 UFT A 24 MG MG A 102 1555 1555 2.39 LINK MG MG A 101 O HOH A 202 1555 1555 1.92 LINK MG MG A 101 O HOH A 203 1555 1555 2.19 LINK MG MG A 101 O HOH A 207 1555 1555 1.99 LINK MG MG A 102 O HOH A 208 1555 1555 2.37 LINK MG MG A 102 O HOH A 212 1555 1555 1.95 SITE 1 AC1 16 LYS H 96 GLU H 97 THR H 98 TYR H 99 SITE 2 AC1 16 PHE H 174 ASP H 189 ALA H 190 GLN H 192 SITE 3 AC1 16 VAL H 213 TRP H 215 GLY H 216 GLU H 217 SITE 4 AC1 16 GLY H 219 GLY H 226 ILE H 227 TYR H 228 SITE 1 AC2 6 TYR H 185 ASP H 185A ARG H 222 LYS H 224 SITE 2 AC2 6 HOH H 419 HOH H 421 SITE 1 AC3 5 ASP H 70 ASN H 72 GLN H 75 GLU H 76 SITE 2 AC3 5 GLU H 80 SITE 1 AC4 6 A A 10 CFL A 22 UFT A 23 HOH A 202 SITE 2 AC4 6 HOH A 203 HOH A 207 SITE 1 AC5 5 A A 10 UFT A 24 G A 25 HOH A 208 SITE 2 AC5 5 HOH A 212 CRYST1 55.744 164.275 124.521 90.00 90.00 90.00 C 2 2 21 8 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 0.017939 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006087 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008031 0.00000