HEADER HYDROLASE/DNA 09-OCT-17 6EO6 TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA-THROMBIN AND TITLE 2 MODIFIED 15-MER DNA APTAMER CONTAINING 5-(3-(2-(1H-INDOL-3-YL) TITLE 3 ACETAMIDE-N-YL)-1-PROPEN-1-YL)-2'-DEOXYURIDINE RESIDUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GA63A - TBA MODIFIED APTAMER; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 15-MER DNA APTAMER SPECIFIC TO HUMAN ALPHA-THROMBIN, COMPND 6 CONTAINING 5-(3-(2-(1H-INDOL-3-YL)ACETAMIDE-N-YL)-1-PROPEN-1-YL)-2'- COMPND 7 DEOXYURIDINE RESIDUE.; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROTHROMBIN; COMPND 10 CHAIN: L; COMPND 11 SYNONYM: COAGULATION FACTOR II; COMPND 12 EC: 3.4.21.5; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PROTHROMBIN; COMPND 15 CHAIN: H; COMPND 16 SYNONYM: COAGULATION FACTOR II; COMPND 17 EC: 3.4.21.5 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS ALPHA THROMBIN, APTAMER, THROMBIN-MTBA, COMPLEX, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.M.DOLOT,B.NAWROT,X.YANG REVDAT 7 17-JAN-24 6EO6 1 HETSYN REVDAT 6 29-JUL-20 6EO6 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 20-FEB-19 6EO6 1 SOURCE REVDAT 4 24-OCT-18 6EO6 1 REMARK LINK REVDAT 3 18-JUL-18 6EO6 1 JRNL REVDAT 2 20-JUN-18 6EO6 1 REMARK REVDAT 1 25-OCT-17 6EO6 0 SPRSDE 25-OCT-17 6EO6 5LUW JRNL AUTH R.DOLOT,C.H.LAM,M.SIERANT,Q.ZHAO,F.W.LIU,B.NAWROT,M.EGLI, JRNL AUTH 2 X.YANG JRNL TITL CRYSTAL STRUCTURES OF THROMBIN IN COMPLEX WITH CHEMICALLY JRNL TITL 2 MODIFIED THROMBIN DNA APTAMERS REVEAL THE ORIGINS OF JRNL TITL 3 ENHANCED AFFINITY. JRNL REF NUCLEIC ACIDS RES. V. 46 4819 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29684204 JRNL DOI 10.1093/NAR/GKY268 REMARK 2 REMARK 2 RESOLUTION. 1.69 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 68190 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3441 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) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.73 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4827 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 286 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2332 REMARK 3 NUCLEIC ACID ATOMS : 330 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -2.26000 REMARK 3 B12 (A**2) : 0.35000 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): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.291 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2931 ; 0.028 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2562 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4043 ; 2.751 ; 1.887 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5969 ; 1.355 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 7.833 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;32.948 ;23.590 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 455 ;14.985 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.475 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 409 ; 0.176 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3070 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 622 ; 0.003 ; 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): 1221 ; 3.681 ; 2.618 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1220 ; 3.522 ; 2.613 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1542 ; 5.276 ; 3.895 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1543 ; 5.274 ; 3.903 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1710 ; 4.568 ; 3.132 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1711 ; 4.567 ; 3.134 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2500 ; 6.622 ; 4.550 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3624 ; 8.911 ;31.988 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3625 ; 8.911 ;31.991 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 : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6EO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1200006945. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 81.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.56300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.3.02 REMARK 200 STARTING MODEL: 1HAO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% W/V PEG4000, 20% V/V 2-PROPANOL, REMARK 280 0.2 M SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 281K 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 83.14000 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 41.57000 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 41.57000 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 83.14000 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: 4180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, L, H 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 328 REMARK 465 PHE L 329 REMARK 465 GLY L 330 REMARK 465 SER L 331 REMARK 465 GLY L 332 REMARK 465 GLY L 362 REMARK 465 ARG L 363 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 ARG H 436 CA ASN H 437 1.53 REMARK 500 CG ASN H 416 C1 NAG H 703 1.74 REMARK 500 OD1 ASN H 416 C1 NAG H 703 1.95 REMARK 500 CG ASN H 416 O5 NAG H 703 2.13 REMARK 500 O ASP L 361 O HOH L 401 2.13 REMARK 500 O HOH H 870 O HOH H 1023 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 DT D 409 O3' DG D 410 P -0.076 REMARK 500 GLU L 333 CD GLU L 333 OE2 0.089 REMARK 500 GLU H 371 CD GLU H 371 OE2 -0.066 REMARK 500 GLN H 378 CD GLN H 378 NE2 -0.161 REMARK 500 ASP H 414 CB ASP H 414 CG -0.161 REMARK 500 ASN H 437 N ASN H 437 CA 0.466 REMARK 500 GLU H 509 CB GLU H 509 CG -0.153 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 DT D 409 O5' - P - OP2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG D 410 O5' - P - OP2 ANGL. DEV. = 9.7 DEGREES REMARK 500 GLU L 333 CG - CD - OE1 ANGL. DEV. = -12.3 DEGREES REMARK 500 GLU L 333 CG - CD - OE2 ANGL. DEV. = 14.6 DEGREES REMARK 500 ASP H 369 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP H 369 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP H 414 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP H 414 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 VAL H 424 CA - CB - CG1 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG H 436 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG H 436 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG H 436 O - C - N ANGL. DEV. = -12.5 DEGREES REMARK 500 ASN H 437 C - N - CA ANGL. DEV. = -40.1 DEGREES REMARK 500 ARG H 452 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG H 452 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG H 456 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ASP H 460 CB - CG - OD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG H 461 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG H 461 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP H 485 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP H 538 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP H 597 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG H 608 NE - CZ - NH1 ANGL. DEV. = 5.2 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 342 -89.47 -132.32 REMARK 500 ILE L 360 -66.65 -92.77 REMARK 500 SER H 385 113.85 -162.13 REMARK 500 CYS H 391 168.28 174.92 REMARK 500 SER H 397 -164.39 -162.50 REMARK 500 TYR H 410 85.79 -153.01 REMARK 500 ASN H 416 81.19 -157.60 REMARK 500 HIS H 429 -58.96 -131.30 REMARK 500 ILE H 438 -58.09 -123.17 REMARK 500 ILE H 438 -65.37 -132.94 REMARK 500 TRP H 511 68.18 -117.58 REMARK 500 THR H 512 -171.24 135.20 REMARK 500 ASN H 514 -72.46 172.99 REMARK 500 VAL H 515 130.94 49.12 REMARK 500 SER H 589 -56.79 -120.91 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 TRP H 511 THR H 512 35.34 REMARK 500 THR H 512 ALA H 513 -45.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D 669 DISTANCE = 7.32 ANGSTROMS REMARK 525 HOH H1102 DISTANCE = 6.45 ANGSTROMS 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 K D 501 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 401 O6 REMARK 620 2 DG D 402 O6 67.6 REMARK 620 3 DG D 405 O6 120.7 70.8 REMARK 620 4 DG D 406 O6 71.7 98.0 74.4 REMARK 620 5 DG D 410 O6 113.6 168.6 100.1 72.4 REMARK 620 6 DG D 411 O6 168.1 112.3 68.8 119.5 69.1 REMARK 620 7 DG D 414 O6 98.6 69.5 104.3 166.7 120.5 71.0 REMARK 620 8 DG D 415 O6 71.2 118.5 167.9 110.1 71.5 99.6 73.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 702 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 596 O REMARK 620 2 LYS H 599 O 95.7 REMARK 620 3 HOH H 879 O 163.1 70.9 REMARK 620 4 HOH H 894 O 103.9 160.3 89.5 REMARK 620 5 HOH H 903 O 87.1 93.2 83.5 85.7 REMARK 620 6 HOH H1001 O 99.6 82.4 89.0 96.3 172.2 REMARK 620 N 1 2 3 4 5 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 701 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL DBREF 6EO6 D 401 415 PDB 6EO6 6EO6 401 415 DBREF 6EO6 L 328 363 UNP P00734 THRB_HUMAN 328 363 DBREF 6EO6 H 364 622 UNP P00734 THRB_HUMAN 364 622 SEQRES 1 D 15 DG DG DT 77Y DG DG DT DG DT DG DG DT DT SEQRES 2 D 15 DG DG 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 HET 77Y D 404 35 HET K D 501 1 HET 0G6 H 701 30 HET NA H 702 1 HET NAG H 703 14 HETNAM 77Y 5-(3-(2-(1H-INDOL-3-YL)ACETAMIDE-N-YL)-1-PROPEN-1-YL)- HETNAM 2 77Y 2'-DEOXYURIDINE HETNAM K POTASSIUM ION 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 NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN 0G6 PPACK HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 77Y C22 H25 N4 O9 P FORMUL 4 K K 1+ FORMUL 5 0G6 C21 H34 CL N6 O3 1+ FORMUL 6 NA NA 1+ FORMUL 7 NAG C8 H15 N O6 FORMUL 8 HOH *412(H2 O) HELIX 1 AA1 PHE L 342 SER L 346 5 5 HELIX 2 AA2 THR L 351 TYR L 359 1 9 HELIX 3 AA3 ALA H 404 CYS H 407 5 4 HELIX 4 AA4 PRO H 411 ASP H 414 5 4 HELIX 5 AA5 THR H 418 ASN H 420 5 3 HELIX 6 AA6 ASP H 485 LEU H 493 1 9 HELIX 7 AA7 GLU H 532 SER H 539 1 8 HELIX 8 AA8 LYS H 554 GLY H 558 5 5 HELIX 9 AA9 LEU H 609 GLY H 621 1 13 SHEET 1 AA1 7 SER H 368 ASP H 369 0 SHEET 2 AA1 7 GLN H 524 PRO H 529 -1 O VAL H 525 N SER H 368 SHEET 3 AA1 7 LYS H 498 GLY H 503 -1 N VAL H 501 O VAL H 526 SHEET 4 AA1 7 PRO H 571 LYS H 575 -1 O VAL H 573 N ARG H 500 SHEET 5 AA1 7 TRP H 582 TRP H 590 -1 O TYR H 583 N MET H 574 SHEET 6 AA1 7 GLY H 601 HIS H 605 -1 O PHE H 602 N TRP H 590 SHEET 7 AA1 7 MET H 548 ALA H 551 -1 N PHE H 549 O TYR H 603 SHEET 1 AA2 7 GLN H 378 ARG H 383 0 SHEET 2 AA2 7 GLU H 388 LEU H 395 -1 O GLU H 388 N ARG H 383 SHEET 3 AA2 7 TRP H 400 THR H 403 -1 O LEU H 402 N SER H 394 SHEET 4 AA2 7 ALA H 464 LEU H 468 -1 O MET H 466 N VAL H 401 SHEET 5 AA2 7 LYS H 440 ILE H 449 -1 N GLU H 445 O LYS H 467 SHEET 6 AA2 7 LEU H 422 ILE H 426 -1 N ILE H 426 O LYS H 440 SHEET 7 AA2 7 GLN H 378 ARG H 383 -1 N PHE H 382 O LEU H 423 SHEET 1 AA3 2 LEU H 409 TYR H 410 0 SHEET 2 AA3 2 LYS H 415 ASN H 416 -1 O LYS H 415 N TYR H 410 SSBOND 1 CYS L 336 CYS H 482 1555 1555 2.08 SSBOND 2 CYS H 391 CYS H 407 1555 1555 2.09 SSBOND 3 CYS H 536 CYS H 550 1555 1555 2.05 SSBOND 4 CYS H 564 CYS H 594 1555 1555 2.06 LINK O3' DT D 403 P 77Y D 404 1555 1555 1.56 LINK O3' 77Y D 404 P DG D 405 1555 1555 1.61 LINK CE1 HIS H 406 C3 0G6 H 701 1555 1555 1.63 LINK ND2 ASN H 416 C1 NAG H 703 1555 1555 1.26 LINK ND2 ASN H 416 O5 NAG H 703 1555 1555 1.47 LINK OG SER H 568 C2 0G6 H 701 1555 1555 1.51 LINK O6 DG D 401 K K D 501 1555 1555 2.75 LINK O6 DG D 402 K K D 501 1555 1555 2.79 LINK O6 DG D 405 K K D 501 1555 1555 2.77 LINK O6 DG D 406 K K D 501 1555 1555 2.79 LINK O6 DG D 410 K K D 501 1555 1555 2.71 LINK O6 DG D 411 K K D 501 1555 1555 2.83 LINK O6 DG D 414 K K D 501 1555 1555 2.83 LINK O6 DG D 415 K K D 501 1555 1555 2.83 LINK O ARG H 596 NA NA H 702 1555 1555 2.34 LINK O LYS H 599 NA NA H 702 1555 1555 2.29 LINK NA NA H 702 O HOH H 879 1555 1555 2.44 LINK NA NA H 702 O HOH H 894 1555 1555 2.39 LINK NA NA H 702 O HOH H 903 1555 1555 2.60 LINK NA NA H 702 O HOH H1001 1555 1555 2.33 CISPEP 1 SER H 385 PRO H 386 0 -7.48 CRYST1 94.095 94.095 124.710 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 0.010628 0.006136 0.000000 0.00000 SCALE2 0.000000 0.012272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008019 0.00000