HEADER HYDROLASE 02-JUN-20 6Z8W TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA THROMBIN AND A TITLE 2 THROMBIN BINDING APTAMER VARIANT (TBA-3G), WHICH CONTAINS 1-BETA-D- TITLE 3 GLUCOPYRANOSYL RESIDUE IN THE SIDE CHAIN OF THY3 AT N3. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTHROMBIN; COMPND 8 CHAIN: H; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TBA-3G; COMPND 13 CHAIN: A; COMPND 14 ENGINEERED: YES 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 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS MODIFIED APTAMER, DNA-PROTEIN COMPLEX, ANTICOAUGULANT, G-QUADRUPLEX, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.TROISI,E.N.TIMOFEEV,F.SICA REVDAT 3 24-JAN-24 6Z8W 1 JRNL REVDAT 2 03-MAR-21 6Z8W 1 JRNL REVDAT 1 27-JAN-21 6Z8W 0 JRNL AUTH I.SMIRNOV,N.KOLGANOVA,R.TROISI,F.SICA,E.TIMOFEEV JRNL TITL EXPANDING THE RECOGNITION INTERFACE OF THE THROMBIN-BINDING JRNL TITL 2 APTAMER HD1 THROUGH MODIFICATION OF RESIDUES T3 AND T12. JRNL REF MOL THER NUCLEIC ACIDS V. 23 863 2021 JRNL REFN ESSN 2162-2531 JRNL PMID 33614235 JRNL DOI 10.1016/J.OMTN.2021.01.004 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 61.5 REMARK 3 NUMBER OF REFLECTIONS : 39863 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2046 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 117 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 2.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2227 REMARK 3 NUCLEIC ACID ATOMS : 312 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.19000 REMARK 3 B12 (A**2) : -0.03000 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.715 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2698 ; 0.016 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3720 ; 2.304 ; 1.604 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 281 ; 7.396 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;30.724 ;21.452 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 400 ;14.528 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;13.181 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 337 ; 0.157 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1973 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 : L 7 L 215 REMARK 3 ORIGIN FOR THE GROUP (A): 47.8321 -12.3798 28.4488 REMARK 3 T TENSOR REMARK 3 T11: 0.0767 T22: 0.0378 REMARK 3 T33: 0.0488 T12: -0.0025 REMARK 3 T13: -0.0007 T23: -0.0293 REMARK 3 L TENSOR REMARK 3 L11: 3.2295 L22: 2.4769 REMARK 3 L33: 3.7924 L12: -0.6241 REMARK 3 L13: 1.8373 L23: -1.3185 REMARK 3 S TENSOR REMARK 3 S11: -0.0412 S12: -0.0056 S13: 0.2924 REMARK 3 S21: 0.0352 S22: -0.0090 S23: -0.0518 REMARK 3 S31: -0.3822 S32: 0.1565 S33: 0.0503 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 : H 37 H 551 REMARK 3 ORIGIN FOR THE GROUP (A): 42.0520 -29.2164 21.0532 REMARK 3 T TENSOR REMARK 3 T11: 0.0102 T22: 0.0120 REMARK 3 T33: 0.0087 T12: 0.0064 REMARK 3 T13: -0.0023 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.4853 L22: 1.1235 REMARK 3 L33: 1.5466 L12: 0.2153 REMARK 3 L13: 0.4853 L23: 0.1535 REMARK 3 S TENSOR REMARK 3 S11: 0.0246 S12: -0.0257 S13: -0.0994 REMARK 3 S21: -0.0002 S22: 0.0266 S23: 0.0284 REMARK 3 S31: 0.0464 S32: -0.0628 S33: -0.0512 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 234 REMARK 3 ORIGIN FOR THE GROUP (A): 69.9060 -31.7904 29.8163 REMARK 3 T TENSOR REMARK 3 T11: 0.0100 T22: 0.0957 REMARK 3 T33: 0.0744 T12: 0.0178 REMARK 3 T13: -0.0003 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 2.5749 L22: 5.0572 REMARK 3 L33: 2.2707 L12: -0.7412 REMARK 3 L13: 0.0677 L23: 0.5519 REMARK 3 S TENSOR REMARK 3 S11: 0.0241 S12: -0.0658 S13: 0.0448 REMARK 3 S21: -0.1256 S22: -0.0361 S23: -0.1936 REMARK 3 S31: -0.0779 S32: 0.0832 S33: 0.0120 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6Z8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41910 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 125.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 20.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1PPB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM KCL, 35% V/V PENTAERYTHRITOL REMARK 280 PROPOXYLATE, 50 MM HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.55067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.77533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.77533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.55067 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, 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 THR L -5 REMARK 465 PHE L -4 REMARK 465 GLY L -3 REMARK 465 SER L -2 REMARK 465 GLY L -1 REMARK 465 GLU L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 REMARK 465 THR H 148A REMARK 465 ALA H 148B REMARK 465 ASN H 148C REMARK 465 VAL H 148D REMARK 465 GLY H 148E REMARK 465 LYS H 148F REMARK 465 GLY H 246 REMARK 465 GLU H 247 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 ARG L 14D CD NE CZ NH1 NH2 REMARK 470 LYS H 87 CE NZ REMARK 470 LYS H 110 CG CD CE NZ REMARK 470 GLU H 127 CG CD OE1 OE2 REMARK 470 LYS H 145 CE NZ REMARK 470 TRP H 148 C O REMARK 470 ARG H 173 CG CD NE CZ NH1 NH2 REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 236 CG CD CE NZ REMARK 470 LYS H 240 CE NZ REMARK 470 DT A 9 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT A 9 C7 C6 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 H 101 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP H 186A CB - CA - C ANGL. DEV. = 14.0 DEGREES REMARK 500 PHE H 245 CA - C - O ANGL. DEV. = -15.2 DEGREES REMARK 500 DG A 5 O5' - C5' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG A 6 O5' - P - OP2 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG A 14 O5' - P - OP1 ANGL. DEV. = -6.7 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 -86.64 -126.78 REMARK 500 TYR H 60A 82.13 -153.99 REMARK 500 ASN H 60G 80.54 -158.67 REMARK 500 HIS H 71 -55.16 -131.76 REMARK 500 GLU H 97A -73.75 -114.44 REMARK 500 ASN H 205 8.99 80.20 REMARK 500 SER H 214 -59.51 -126.24 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 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221 O REMARK 620 2 LYS H 224 O 91.6 REMARK 620 3 HOH H 411 O 160.6 73.5 REMARK 620 4 HOH H 427 O 104.1 164.3 91.4 REMARK 620 5 HOH H 446 O 87.5 93.9 81.5 87.6 REMARK 620 6 HOH H 519 O 96.1 80.3 93.5 97.1 173.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 2 O6 67.4 REMARK 620 3 DG A 5 O6 120.7 71.9 REMARK 620 4 DG A 6 O6 71.0 97.6 73.8 REMARK 620 5 DG A 10 O6 113.7 169.2 99.5 73.4 REMARK 620 6 DG A 11 O6 169.7 110.9 66.6 119.2 69.9 REMARK 620 7 DG A 14 O6 98.0 67.6 104.3 164.5 121.8 72.4 REMARK 620 8 DG A 15 O6 72.4 118.2 166.7 111.4 71.4 100.7 74.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 630 REMARK 630 MOLECULE TYPE: NULL 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 301 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 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 K A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QCK A 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Z8V RELATED DB: PDB REMARK 900 SAME PROTEIN WITH ANOTHER TBA VARIANT REMARK 900 RELATED ID: 6Z8X RELATED DB: PDB REMARK 900 SAME PROTEIN WITH ANOTHER TBA VARIANT DBREF 6Z8W L -5 17 UNP P00734 THRB_HUMAN 328 363 DBREF 6Z8W H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 6Z8W A 1 2 PDB 6Z8W 6Z8W 1 2 DBREF 6Z8W A 3 15 PDB 6Z8W 6Z8W 3 15 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 A 15 DG DG QCK DT DG DG DT DG DT DG DG DT DT SEQRES 2 A 15 DG DG HET QCK A 3 26 HET 0G6 H 301 30 HET NA H 302 1 HET K A 101 1 HETNAM QCK (4-METHYLTRIAZOLE)-THYMIDINE-5'-MONOPHOSPHATE 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 K POTASSIUM ION HETSYN 0G6 PPACK FORMUL 3 QCK C13 H18 N5 O8 P FORMUL 4 0G6 C21 H34 CL N6 O3 1+ FORMUL 5 NA NA 1+ FORMUL 6 K K 1+ FORMUL 7 HOH *200(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 SER H 171 1 8 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 PHE H 245 1 12 SHEET 1 AA1 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 GLN H 30 ARG H 35 0 SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52 SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N TYR H 89 O LEU H 105 SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 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 2.18 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.16 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.06 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.19 LINK NE2 HIS H 57 C3 0G6 H 301 1555 1555 1.53 LINK OG SER H 195 C2 0G6 H 301 1555 1555 1.43 LINK O3' DG A 2 P QCK A 3 1555 1555 1.60 LINK O3' QCK A 3 P DT A 4 1555 1555 1.56 LINK O ARG H 221 NA NA H 302 1555 1555 2.38 LINK O LYS H 224 NA NA H 302 1555 1555 2.39 LINK NA NA H 302 O HOH H 411 1555 1555 2.38 LINK NA NA H 302 O HOH H 427 1555 1555 2.50 LINK NA NA H 302 O HOH H 446 1555 1555 2.85 LINK NA NA H 302 O HOH H 519 1555 1555 2.26 LINK O6 DG A 1 K K A 101 1555 1555 2.82 LINK O6 DG A 2 K K A 101 1555 1555 2.78 LINK O6 DG A 5 K K A 101 1555 1555 2.76 LINK O6 DG A 6 K K A 101 1555 1555 2.78 LINK O6 DG A 10 K K A 101 1555 1555 2.60 LINK O6 DG A 11 K K A 101 1555 1555 2.92 LINK O6 DG A 14 K K A 101 1555 1555 2.85 LINK O6 DG A 15 K K A 101 1555 1555 2.79 CISPEP 1 SER H 36A PRO H 37 0 -8.10 SITE 1 AC1 17 HIS H 57 TYR H 60A GLU H 97A ASP H 189 SITE 2 AC1 17 ALA H 190 GLY H 193 SER H 195 SER H 214 SITE 3 AC1 17 TRP H 215 GLY H 216 GLY H 219 GLY H 226 SITE 4 AC1 17 HOH H 421 HOH H 433 HOH H 490 HOH H 496 SITE 5 AC1 17 HOH H 497 SITE 1 AC2 6 ARG H 221 LYS H 224 HOH H 411 HOH H 427 SITE 2 AC2 6 HOH H 446 HOH H 519 SITE 1 AC3 8 DG A 1 DG A 2 DG A 5 DG A 6 SITE 2 AC3 8 DG A 10 DG A 11 DG A 14 DG A 15 SITE 1 AC4 4 DG A 2 DT A 4 TYR H 76 ILE H 82 CRYST1 94.798 94.798 125.326 90.00 90.00 120.00 P 32 2 1 6 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 0.010549 0.006090 0.000000 0.00000 SCALE2 0.000000 0.012181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007979 0.00000