HEADER HYDROLASE/HYDROLASE INHIBITOR 06-APR-18 6CYM TITLE REVERSIBLE COVALENT DIRECT THROMBIN INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A, C; 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: B, D; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5 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 KEYWDS HYDROLASE, BLOOD COAGULATION, PLASMA, CALCIUM-BINDING, GLYCOPROTEIN, KEYWDS 2 SERINE PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.SIVARAJA,D.C.WILLIAMS REVDAT 3 29-JUL-20 6CYM 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 15-AUG-18 6CYM 1 JRNL REVDAT 1 09-MAY-18 6CYM 0 JRNL AUTH M.SIVARAJA,N.POZZI,M.RIENZO,K.LIN,T.P.SHIAU,D.M.CLEMENS, JRNL AUTH 2 L.IGOUDIN,P.ZALICKI,S.S.CHANG,M.A.ESTIARTE,K.M.SHORT, JRNL AUTH 3 D.C.WILLIAMS,A.DATTA,E.DI CERA,D.B.KITA JRNL TITL REVERSIBLE COVALENT DIRECT THROMBIN INHIBITORS. JRNL REF PLOS ONE V. 13 01377 2018 JRNL REFN ESSN 1932-6203 JRNL PMID 30071045 JRNL DOI 10.1371/JOURNAL.PONE.0201377 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 3 NUMBER OF REFLECTIONS : 10936 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) : 0.176 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 566 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 36.04 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1287 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2100 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1220 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE : 0.3143 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.21 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4556 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.97550 REMARK 3 B22 (A**2) : 8.70760 REMARK 3 B33 (A**2) : -2.73220 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.350 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.521 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.856 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4712 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6361 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1670 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 112 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 671 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4712 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 579 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5212 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.19 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.89 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.45 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { B|1 - B|27 } REMARK 3 ORIGIN FOR THE GROUP (A): 12.2051 38.7551 14.9259 REMARK 3 T TENSOR REMARK 3 T11: -0.1993 T22: 0.1434 REMARK 3 T33: 0.0120 T12: -0.2387 REMARK 3 T13: -0.0297 T23: -0.0702 REMARK 3 L TENSOR REMARK 3 L11: 1.2852 L22: 0.4815 REMARK 3 L33: 5.1777 L12: 1.2676 REMARK 3 L13: 2.2618 L23: -1.0776 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: 0.0147 S13: 0.1549 REMARK 3 S21: 0.2061 S22: 0.1386 S23: -0.5442 REMARK 3 S31: -0.5320 S32: 0.2907 S33: -0.1427 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|15 - A|271 } REMARK 3 ORIGIN FOR THE GROUP (A): 2.3465 28.4197 2.2338 REMARK 3 T TENSOR REMARK 3 T11: -0.3465 T22: 0.0663 REMARK 3 T33: -0.2542 T12: -0.0174 REMARK 3 T13: 0.0354 T23: -0.0417 REMARK 3 L TENSOR REMARK 3 L11: 3.5580 L22: 2.0674 REMARK 3 L33: 4.0502 L12: -0.7493 REMARK 3 L13: 0.0829 L23: 0.4207 REMARK 3 S TENSOR REMARK 3 S11: 0.1166 S12: 0.5591 S13: 0.1481 REMARK 3 S21: -0.1790 S22: 0.0110 S23: -0.1453 REMARK 3 S31: -0.0588 S32: 0.1112 S33: -0.1275 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { D|1 - D|27 } REMARK 3 ORIGIN FOR THE GROUP (A): 33.2503 22.8933 43.1849 REMARK 3 T TENSOR REMARK 3 T11: -0.4782 T22: 0.5630 REMARK 3 T33: -0.1234 T12: 0.1035 REMARK 3 T13: -0.0730 T23: 0.0833 REMARK 3 L TENSOR REMARK 3 L11: 5.6587 L22: 1.3660 REMARK 3 L33: 6.4914 L12: 1.2935 REMARK 3 L13: 0.9650 L23: -1.9039 REMARK 3 S TENSOR REMARK 3 S11: 0.0520 S12: 0.0252 S13: 0.0996 REMARK 3 S21: -0.0383 S22: -0.0544 S23: -0.4859 REMARK 3 S31: 0.0682 S32: 0.0706 S33: 0.0024 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { C|15 - C|271 } REMARK 3 ORIGIN FOR THE GROUP (A): 19.2086 12.1500 35.8613 REMARK 3 T TENSOR REMARK 3 T11: -0.3331 T22: 0.1296 REMARK 3 T33: -0.3748 T12: 0.3040 REMARK 3 T13: -0.0740 T23: -0.1172 REMARK 3 L TENSOR REMARK 3 L11: 4.0126 L22: 2.4302 REMARK 3 L33: 5.3978 L12: -0.5981 REMARK 3 L13: 1.8513 L23: 0.3431 REMARK 3 S TENSOR REMARK 3 S11: 0.4630 S12: 0.7828 S13: -0.6963 REMARK 3 S21: -0.2097 S22: -0.1113 S23: -0.2226 REMARK 3 S31: 1.0885 S32: 0.9820 S33: -0.3518 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6CYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-16 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10936 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: FOR COMPLEX FORMATION, 2 MG HUMAN REMARK 280 ALPHA-THROMBIN (7.1 MG/ML IN 50% V/V GLYCEROL) WERE MIXED WITH REMARK 280 0.5 MM COMPOUND 1 IN DMSO AND DIALYZED OVERNIGHT INTO A SOLUTION REMARK 280 OF 20 MM SODIUM CITRATE AND 1.3 MM NA2SO4 (PH 5.8). AFTER REMARK 280 DIALYSIS, ANOTHER 0.5 MM COMPOUND WERE ADDED AND LEFT TO REMARK 280 INCUBATE AT ROOM TEMPERATURE FOR 1 H. THE PROTEIN WAS REMARK 280 CENTRIFUGED FOR 5 MIN AT 4 DEG C AND 8000X RCF. THE PELLET, REMARK 280 INCLUDING ABOUT 120 UL OF BUFFER, WAS MIXED WITH 100 UL OF A REMARK 280 SOLUTION CONTAINING 50 MM SODIUM PHOSPHATE (PH 7.3), 190 MM REMARK 280 SODIUM CHLORIDE, AND 0.2 MM COMPOUND 1. THE CRYSTAL USED FOR REMARK 280 DATA COLLECTION WAS GROWN FROM THE JCSG+ SCREEN IN WELL A10. THE REMARK 280 CRYSTAL WAS GROWN AT 20 DEG C USING A MRC 3-WELL PLATE AND IN A REMARK 280 150 + 150 NL DROP WITH A RESERVOIR OF 0.2 M POTASSIUM FORMATE REMARK 280 AND 20% W/V PEG-3350., BATCH MODE, TEMPERATURE 294K 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 73.00500 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 73.00500 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 45.83500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.86500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.83500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.86500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.00500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.83500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.86500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.00500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.83500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.86500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 TRP A 162 REMARK 465 THR A 163 REMARK 465 ALA A 164 REMARK 465 ASN A 165 REMARK 465 VAL A 166 REMARK 465 GLY A 167 REMARK 465 LYS A 168 REMARK 465 GLY A 272 REMARK 465 GLU A 273 REMARK 465 ASP B 28 REMARK 465 GLY C 272 REMARK 465 GLU C 273 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 OG SER A 219 O9 71F A 300 2.06 REMARK 500 OG SER C 219 O9 71F C 301 2.18 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 LEU A 41 -67.63 -100.72 REMARK 500 SER A 48 -169.38 -165.22 REMARK 500 TYR A 61 79.36 -150.55 REMARK 500 ASP A 65 47.31 37.18 REMARK 500 HIS A 80 -57.48 -122.32 REMARK 500 THR A 83 -76.69 -85.32 REMARK 500 ARG A 87 -95.97 -34.17 REMARK 500 ILE A 89 -68.64 -138.65 REMARK 500 GLU A 108 -48.26 -146.22 REMARK 500 ASN A 109 3.05 -152.15 REMARK 500 SER A 126 -156.07 -146.62 REMARK 500 VAL A 239 101.97 -56.22 REMARK 500 SER A 240 -78.05 -95.61 REMARK 500 PHE B 9 -84.64 -116.29 REMARK 500 LEU C 41 -66.53 -100.46 REMARK 500 SER C 48 -168.60 -164.35 REMARK 500 TYR C 61 79.58 -150.95 REMARK 500 ASP C 65 48.88 36.19 REMARK 500 HIS C 80 -56.61 -125.95 REMARK 500 THR C 83 -75.33 -87.68 REMARK 500 ARG C 87 -82.56 -32.26 REMARK 500 GLU C 108 -48.78 -144.90 REMARK 500 ASN C 109 4.08 -150.82 REMARK 500 SER C 126 -155.66 -148.22 REMARK 500 GLU C 160 -37.12 -37.76 REMARK 500 CYS C 215 -160.37 -123.07 REMARK 500 VAL C 239 102.77 -54.92 REMARK 500 SER C 240 -78.40 -97.82 REMARK 500 PHE D 9 -85.30 -116.24 REMARK 500 LYS D 17 -30.52 -38.62 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 A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 247 O REMARK 620 2 LYS A 250 O 67.9 REMARK 620 3 HOH A 401 O 144.2 95.3 REMARK 620 4 HOH A 405 O 84.8 64.9 59.4 REMARK 620 5 HOH A 406 O 87.0 116.5 128.5 170.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG C 247 O REMARK 620 2 LYS C 250 O 78.8 REMARK 620 N 1 DBREF 6CYM A 15 273 UNP P00734 THRB_HUMAN 364 622 DBREF 6CYM B 1 28 UNP P00734 THRB_HUMAN 334 361 DBREF 6CYM C 15 273 UNP P00734 THRB_HUMAN 364 622 DBREF 6CYM D 1 28 UNP P00734 THRB_HUMAN 334 361 SEQRES 1 A 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 A 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 A 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 A 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 A 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 A 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 A 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 A 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 A 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 A 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 A 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 A 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 A 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 A 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 A 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 A 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 A 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 A 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 A 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 A 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 B 28 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 B 28 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 B 28 ILE ASP SEQRES 1 C 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 C 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 C 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 C 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 C 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 C 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 C 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 C 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 C 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 C 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 C 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 C 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 C 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 C 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 C 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 C 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 C 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 C 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 C 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 C 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 D 28 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 D 28 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 D 28 ILE ASP HET 71F A 300 10 HET NAG A 301 14 HET NA A 302 1 HET 71F C 301 10 HET NA C 302 1 HETNAM 71F 2-METHOXYBENZOIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION FORMUL 5 71F 2(C8 H8 O3) FORMUL 6 NAG C8 H15 N O6 FORMUL 7 NA 2(NA 1+) FORMUL 10 HOH *22(H2 O) HELIX 1 AA1 ALA A 55 CYS A 58 5 4 HELIX 2 AA2 PRO A 62 ASP A 65 5 4 HELIX 3 AA3 THR A 69 ASN A 71 5 3 HELIX 4 AA4 ASP A 136 LEU A 144 1 9 HELIX 5 AA5 GLU A 183 THR A 191 1 9 HELIX 6 AA6 LEU A 260 PHE A 271 1 12 HELIX 7 AA7 THR B 18 TYR B 26 1 9 HELIX 8 AA8 ALA C 55 CYS C 58 5 4 HELIX 9 AA9 PRO C 62 ASP C 65 5 4 HELIX 10 AB1 THR C 69 ASN C 71 5 3 HELIX 11 AB2 ASP C 136 LEU C 144 1 9 HELIX 12 AB3 GLU C 183 THR C 191 1 9 HELIX 13 AB4 LYS C 205 GLY C 209 5 5 HELIX 14 AB5 LEU C 260 ASP C 269 1 10 HELIX 15 AB6 THR D 18 TYR D 26 1 9 SHEET 1 AA1 8 SER A 19 ASP A 20 0 SHEET 2 AA1 8 GLN A 175 VAL A 182 -1 O VAL A 176 N SER A 19 SHEET 3 AA1 8 MET A 199 ALA A 202 -1 O CYS A 201 N VAL A 182 SHEET 4 AA1 8 GLY A 252 HIS A 256 -1 O TYR A 254 N PHE A 200 SHEET 5 AA1 8 TRP A 233 TRP A 241 -1 N TRP A 241 O PHE A 253 SHEET 6 AA1 8 PRO A 222 LYS A 226 -1 N MET A 225 O TYR A 234 SHEET 7 AA1 8 LYS A 149 GLY A 154 -1 N ARG A 151 O VAL A 224 SHEET 8 AA1 8 GLN A 175 VAL A 182 -1 O VAL A 177 N VAL A 152 SHEET 1 AA2 6 LEU A 40 SER A 45 0 SHEET 2 AA2 6 GLN A 29 ARG A 34 -1 N LEU A 32 O LEU A 41 SHEET 3 AA2 6 LEU A 73 ILE A 77 -1 O LEU A 74 N PHE A 33 SHEET 4 AA2 6 LYS A 91 ILE A 100 -1 O LYS A 91 N ILE A 77 SHEET 5 AA2 6 ALA A 115 LEU A 119 -1 O LYS A 118 N GLU A 96 SHEET 6 AA2 6 TRP A 51 THR A 54 -1 N VAL A 52 O MET A 117 SHEET 1 AA3 2 LEU A 60 TYR A 61 0 SHEET 2 AA3 2 LYS A 66 ASN A 67 -1 O LYS A 66 N TYR A 61 SHEET 1 AA4 8 SER C 19 ASP C 20 0 SHEET 2 AA4 8 GLN C 175 VAL C 182 -1 O VAL C 176 N SER C 19 SHEET 3 AA4 8 MET C 199 ALA C 202 -1 O CYS C 201 N VAL C 182 SHEET 4 AA4 8 GLY C 252 HIS C 256 -1 O TYR C 254 N PHE C 200 SHEET 5 AA4 8 TRP C 233 TRP C 241 -1 N TRP C 241 O PHE C 253 SHEET 6 AA4 8 PRO C 222 LYS C 226 -1 N MET C 225 O TYR C 234 SHEET 7 AA4 8 LYS C 149 GLY C 154 -1 N ARG C 151 O VAL C 224 SHEET 8 AA4 8 GLN C 175 VAL C 182 -1 O VAL C 177 N VAL C 152 SHEET 1 AA5 6 GLU C 39 SER C 45 0 SHEET 2 AA5 6 GLN C 29 ARG C 34 -1 N LEU C 32 O LEU C 41 SHEET 3 AA5 6 LEU C 73 ILE C 77 -1 O LEU C 74 N PHE C 33 SHEET 4 AA5 6 LYS C 91 ILE C 100 -1 O LYS C 91 N ILE C 77 SHEET 5 AA5 6 ALA C 115 LEU C 119 -1 O LYS C 118 N GLU C 96 SHEET 6 AA5 6 TRP C 51 THR C 54 -1 N VAL C 52 O MET C 117 SHEET 1 AA6 2 LEU C 60 TYR C 61 0 SHEET 2 AA6 2 LYS C 66 ASN C 67 -1 O LYS C 66 N TYR C 61 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.04 SSBOND 2 CYS A 133 CYS B 3 1555 1555 2.06 SSBOND 3 CYS A 187 CYS A 201 1555 1555 2.04 SSBOND 4 CYS A 215 CYS A 245 1555 1555 2.07 SSBOND 5 CYS C 42 CYS C 58 1555 1555 2.03 SSBOND 6 CYS C 133 CYS D 3 1555 1555 2.05 SSBOND 7 CYS C 187 CYS C 201 1555 1555 2.05 SSBOND 8 CYS C 215 CYS C 245 1555 1555 2.05 LINK ND2 ASN A 67 C1 NAG A 301 1555 1555 1.44 LINK OG SER A 219 C8 71F A 300 1555 1555 1.52 LINK OG SER C 219 C8 71F C 301 1555 1555 1.56 LINK O ARG A 247 NA NA A 302 1555 1555 2.89 LINK O LYS A 250 NA NA A 302 1555 1555 2.73 LINK NA NA A 302 O HOH A 401 1555 1555 3.16 LINK NA NA A 302 O HOH A 405 1555 1555 2.64 LINK NA NA A 302 O HOH A 406 1555 1555 2.94 LINK O ARG C 247 NA NA C 302 1555 1555 2.44 LINK O LYS C 250 NA NA C 302 1555 1555 2.58 CISPEP 1 SER A 36 PRO A 37 0 -4.64 CISPEP 2 SER C 36 PRO C 37 0 -3.75 CRYST1 91.670 99.730 146.010 90.00 90.00 90.00 C 2 2 21 16 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 0.010909 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010027 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006849 0.00000