HEADER PLANT PROTEIN 26-MAY-16 5L4R TITLE X-RAY STRUCTURE OF THE ADDUCT BETWEEN THAUMATIN AND CISPLATIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THAUMATIN I; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THAUMATOCOCCUS DANIELLII; SOURCE 3 ORGANISM_COMMON: KATEMFE; SOURCE 4 ORGANISM_TAXID: 4621; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CISPLATIN, DRUG, MODEL PROTEIN, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.RUSSO KRAUSS,G.FERRARO,A.MERLINO REVDAT 2 10-JAN-24 5L4R 1 LINK REVDAT 1 07-DEC-16 5L4R 0 JRNL AUTH I.RUSSO KRAUSS,G.FERRARO,A.MERLINO JRNL TITL CISPLATIN-PROTEIN INTERACTIONS: UNEXPECTED DRUG BINDING TO JRNL TITL 2 N-TERMINAL AMINE AND LYSINE SIDE CHAINS. JRNL REF INORG.CHEM. V. 55 7814 2016 JRNL REFN ISSN 0020-1669 JRNL PMID 27482735 JRNL DOI 10.1021/ACS.INORGCHEM.6B01234 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 41675 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) : 0.114 REMARK 3 R VALUE (WORKING SET) : 0.112 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2147 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2375 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1551 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 423 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : -0.79000 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.032 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.966 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1746 ; 0.037 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2363 ; 2.904 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 6.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;35.970 ;22.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 273 ;12.101 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.379 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 256 ; 0.264 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1339 ; 0.017 ; 0.021 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): 842 ; 2.730 ; 1.513 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1055 ; 2.934 ; 2.269 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 904 ; 5.048 ; 1.891 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): 3234 ; 6.356 ;17.124 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): 1746 ; 9.570 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 69 ;46.270 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2069 ;18.377 ; 5.000 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5L4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200000071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43868 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 53.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.46600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 3QY5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % PEG3350, 0.2 M SODIUM TARTRATE. REMARK 280 CRYSTALS OF THE ADDUCT WERE OBTAINED BY SOAKING PROCEDURE, REMARK 280 ADDING 1 UL OF CISPLATIN SOLUTION 10 MM TO THE DROP CONTAINING REMARK 280 THAUMATIN CRYSTALS, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 75.07950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.91850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.91850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.53975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.91850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.91850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.61925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.91850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.91850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.53975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.91850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.91850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.61925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.07950 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 N1 73M A 509 O HOH A 605 2.08 REMARK 500 O HOH A 798 O HOH A 799 2.14 REMARK 500 NH2 ARG A 122 O HOH A 607 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 857 O HOH A 1011 4554 1.79 REMARK 500 O HOH A 816 O HOH A 835 6444 1.94 REMARK 500 O HOH A 875 O HOH A 1011 4554 2.10 REMARK 500 N1 CPT A 510 O HOH A 752 6444 2.16 REMARK 500 O HOH A 844 O HOH A 977 4554 2.17 REMARK 500 O HOH A 611 O HOH A 690 6444 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 ARG A 82 CZ ARG A 82 NH2 -0.088 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 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = 10.6 DEGREES REMARK 500 ASP A 98 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 LYS A 106 CD - CE - NZ ANGL. DEV. = -15.1 DEGREES REMARK 500 MET A 112 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 LYS A 163 O - C - N ANGL. DEV. = -12.4 DEGREES REMARK 500 CYS A 164 C - N - CA ANGL. DEV. = 23.4 DEGREES REMARK 500 ARG A 171 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 179 CB - CG - OD2 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 ASP A 25 -136.89 52.85 REMARK 500 CYS A 71 73.28 -117.29 REMARK 500 CYS A 164 152.51 14.10 REMARK 500 CYS A 164 152.51 171.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 163 -10.72 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 A1019 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A1020 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1021 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A1022 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A1023 DISTANCE = 6.95 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 73M A 503 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 1 N REMARK 620 2 73M A 503 N1 88.8 REMARK 620 3 73M A 503 CL1 177.3 91.2 REMARK 620 4 73M A 503 O2 90.0 178.6 90.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 513 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 19 NZ REMARK 620 2 CPT A 513 N1 100.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 510 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 42 OE2 REMARK 620 2 CPT A 510 N1 171.9 REMARK 620 3 CPT A 510 N2 91.2 85.3 REMARK 620 4 CPT A 510 CL1 89.4 93.6 175.8 REMARK 620 5 HOH A 654 O 77.6 107.5 161.7 22.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 506 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 49 NZ REMARK 620 2 CPT A 506 N1 100.4 REMARK 620 3 CPT A 506 CL2 80.5 179.0 REMARK 620 4 CPT A 506 CL1 173.0 86.4 92.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 506 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 49 NZ REMARK 620 2 CPT A 506 N1 76.2 REMARK 620 3 CPT A 506 CL2 94.3 111.3 REMARK 620 4 CPT A 506 CL1 118.1 54.0 75.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 507 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 97 NZ REMARK 620 2 CPT A 507 N1 48.4 REMARK 620 3 CPT A 507 N2 69.0 27.0 REMARK 620 4 CPT A 507 CL1 25.0 33.9 60.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 507 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 97 NZ REMARK 620 2 CPT A 507 N1 160.0 REMARK 620 3 CPT A 507 N2 102.4 90.0 REMARK 620 4 CPT A 507 CL1 77.9 89.6 179.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 504 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 106 NZ REMARK 620 2 CPT A 504 N1 38.0 REMARK 620 3 CPT A 504 N2 38.0 28.9 REMARK 620 4 CPT A 504 CL1 33.1 30.7 53.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 504 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 106 NZ REMARK 620 2 CPT A 504 N1 172.8 REMARK 620 3 CPT A 504 N2 93.3 89.8 REMARK 620 4 CPT A 504 CL1 88.4 88.7 178.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 504 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 106 NZ REMARK 620 2 CPT A 504 N1 69.2 REMARK 620 3 CPT A 504 N2 31.9 37.3 REMARK 620 4 CPT A 504 CL1 91.1 27.1 61.1 REMARK 620 5 HOH A 601 O 119.3 165.9 149.3 149.5 REMARK 620 6 HOH A 603 O 146.7 106.8 136.0 79.7 72.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 508 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 137 NZ REMARK 620 2 CPT A 508 N1 160.1 REMARK 620 3 CPT A 508 N2 87.6 90.6 REMARK 620 4 CPT A 508 CL1 91.9 90.5 178.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 73M A 505 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 168 OE2 REMARK 620 2 73M A 505 N1 99.3 REMARK 620 3 73M A 505 N2 174.0 86.7 REMARK 620 4 73M A 505 O2 81.9 178.8 92.1 REMARK 620 5 HOH A 602 O 86.1 23.2 99.5 157.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 73M A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 73M A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 73M A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPT A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 514 DBREF 5L4R A 1 207 UNP P02883 THM1_THADA 1 207 SEQRES 1 A 207 ALA THR PHE GLU ILE VAL ASN ARG CYS SER TYR THR VAL SEQRES 2 A 207 TRP ALA ALA ALA SER LYS GLY ASP ALA ALA LEU ASP ALA SEQRES 3 A 207 GLY GLY ARG GLN LEU ASN SER GLY GLU SER TRP THR ILE SEQRES 4 A 207 ASN VAL GLU PRO GLY THR ASN GLY GLY LYS ILE TRP ALA SEQRES 5 A 207 ARG THR ASP CYS TYR PHE ASP ASP SER GLY SER GLY ILE SEQRES 6 A 207 CYS LYS THR GLY ASP CYS GLY GLY LEU LEU ARG CYS LYS SEQRES 7 A 207 ARG PHE GLY ARG PRO PRO THR THR LEU ALA GLU PHE SER SEQRES 8 A 207 LEU ASN GLN TYR GLY LYS ASP TYR ILE ASP ILE SER ASN SEQRES 9 A 207 ILE LYS GLY PHE ASN VAL PRO MET ASN PHE SER PRO THR SEQRES 10 A 207 THR ARG GLY CYS ARG GLY VAL ARG CYS ALA ALA ASP ILE SEQRES 11 A 207 VAL GLY GLN CYS PRO ALA LYS LEU LYS ALA PRO GLY GLY SEQRES 12 A 207 GLY CYS ASN ASP ALA CYS THR VAL PHE GLN THR SER GLU SEQRES 13 A 207 TYR CYS CYS THR THR GLY LYS CYS GLY PRO THR GLU TYR SEQRES 14 A 207 SER ARG PHE PHE LYS ARG LEU CYS PRO ASP ALA PHE SER SEQRES 15 A 207 TYR VAL LEU ASP LYS PRO THR THR VAL THR CYS PRO GLY SEQRES 16 A 207 SER SER ASN TYR ARG VAL THR PHE CYS PRO THR ALA HET TLA A 501 10 HET TLA A 502 10 HET 73M A 503 4 HET CPT A 504 10 HET 73M A 505 4 HET CPT A 506 8 HET CPT A 507 5 HET CPT A 508 4 HET 73M A 509 5 HET CPT A 510 4 HET CPT A 511 1 HET CPT A 512 1 HET CPT A 513 2 HET GOL A 514 6 HETNAM TLA L(+)-TARTARIC ACID HETNAM 73M BIS(AZANYL)-CHLORANYL-OXIDANYL-PLATINUM HETNAM CPT CISPLATIN HETNAM GOL GLYCEROL HETSYN CPT DIAMMINE(DICHLORO)PLATINUM HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 TLA 2(C4 H6 O6) FORMUL 4 73M 3(CL H5 N2 O PT) FORMUL 5 CPT 8(CL2 H6 N2 PT) FORMUL 15 GOL C3 H8 O3 FORMUL 16 HOH *423(H2 O) HELIX 1 AA1 ASP A 129 CYS A 134 1 6 HELIX 2 AA2 PRO A 135 LYS A 139 5 5 HELIX 3 AA3 ASP A 147 GLN A 153 1 7 HELIX 4 AA4 THR A 154 CYS A 159 1 6 HELIX 5 AA5 THR A 167 CYS A 177 1 11 SHEET 1 AA1 5 SER A 36 ASN A 40 0 SHEET 2 AA1 5 THR A 2 ASN A 7 -1 N ILE A 5 O TRP A 37 SHEET 3 AA1 5 TYR A 199 PHE A 203 1 O VAL A 201 N VAL A 6 SHEET 4 AA1 5 MET A 112 PRO A 116 -1 N SER A 115 O ARG A 200 SHEET 5 AA1 5 VAL A 124 CYS A 126 -1 O VAL A 124 N PHE A 114 SHEET 1 AA2 4 ALA A 23 LEU A 31 0 SHEET 2 AA2 4 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 AA2 4 GLY A 48 PHE A 58 -1 O LYS A 49 N SER A 18 SHEET 4 AA2 4 GLY A 64 THR A 68 -1 O ILE A 65 N TYR A 57 SHEET 1 AA3 6 ALA A 23 LEU A 31 0 SHEET 2 AA3 6 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 AA3 6 GLY A 48 PHE A 58 -1 O LYS A 49 N SER A 18 SHEET 4 AA3 6 LEU A 87 GLN A 94 -1 O ALA A 88 N ILE A 50 SHEET 5 AA3 6 LYS A 97 SER A 103 -1 O LYS A 97 N GLN A 94 SHEET 6 AA3 6 VAL A 191 PRO A 194 -1 O CYS A 193 N ASP A 98 SSBOND 1 CYS A 9 CYS A 204 1555 1555 2.05 SSBOND 2 CYS A 56 CYS A 66 1555 1555 2.05 SSBOND 3 CYS A 71 CYS A 77 1555 1555 2.01 SSBOND 4 CYS A 121 CYS A 193 1555 1555 2.09 SSBOND 5 CYS A 126 CYS A 177 1555 1555 2.04 SSBOND 6 CYS A 134 CYS A 145 1555 1555 2.05 SSBOND 7 CYS A 149 CYS A 158 1555 1555 2.04 SSBOND 8 CYS A 159 CYS A 164 1555 1555 2.04 LINK N ALA A 1 PT1 73M A 503 1555 1555 2.09 LINK NZ LYS A 19 PT1 CPT A 513 1555 1555 2.41 LINK OE2BGLU A 42 PT1 CPT A 510 1555 1555 2.15 LINK NZ LYS A 49 PT1 ACPT A 506 1555 1555 2.57 LINK NZ LYS A 49 PT1 BCPT A 506 1555 1555 2.38 LINK NZ LYS A 67 PT1 ACPT A 511 1555 1555 2.50 LINK NZ LYS A 97 PT1 BCPT A 507 1555 1555 2.46 LINK NZ LYS A 97 PT1 ACPT A 507 1555 1555 2.24 LINK NZ LYS A 106 PT1 CCPT A 504 1555 1555 2.79 LINK NZ LYS A 106 PT1 ACPT A 504 1555 1555 2.02 LINK NZ LYS A 106 PT1 BCPT A 504 1555 1555 2.55 LINK NZ LYS A 137 PT1 CPT A 508 1555 1555 2.22 LINK NZ LYS A 139 PT1 ACPT A 512 1555 1555 2.61 LINK OE2 GLU A 168 PT1 73M A 505 1555 1555 2.05 LINK PT1 BCPT A 504 O HOH A 601 1555 1555 1.95 LINK PT1 BCPT A 504 O HOH A 603 1555 1555 2.78 LINK PT1 73M A 505 O HOH A 602 1555 1555 2.53 LINK PT1 CPT A 510 O BHOH A 654 1555 1555 2.08 CISPEP 1 PRO A 83 PRO A 84 0 7.12 SITE 1 AC1 13 GLY A 96 LYS A 97 ALA A 136 PRO A 194 SITE 2 AC1 13 GLY A 195 HOH A 610 HOH A 641 HOH A 669 SITE 3 AC1 13 HOH A 696 HOH A 807 HOH A 828 HOH A 881 SITE 4 AC1 13 HOH A 992 SITE 1 AC2 12 ARG A 29 GLU A 35 SER A 36 PHE A 152 SITE 2 AC2 12 TYR A 157 HOH A 657 HOH A 664 HOH A 687 SITE 3 AC2 12 HOH A 756 HOH A 818 HOH A 852 HOH A 856 SITE 1 AC3 8 ALA A 1 VAL A 41 73M A 505 CPT A 510 SITE 2 AC3 8 HOH A 614 HOH A 685 HOH A 700 HOH A 757 SITE 1 AC4 14 ARG A 82 PRO A 83 LYS A 106 CYS A 149 SITE 2 AC4 14 THR A 150 CPT A 506 HOH A 601 HOH A 603 SITE 3 AC4 14 HOH A 688 HOH A 704 HOH A 836 HOH A 850 SITE 4 AC4 14 HOH A 851 HOH A 867 SITE 1 AC5 10 GLU A 168 SER A 196 73M A 503 HOH A 602 SITE 2 AC5 10 HOH A 615 HOH A 683 HOH A 700 HOH A 745 SITE 3 AC5 10 HOH A 771 HOH A 861 SITE 1 AC6 10 GLY A 47 LYS A 49 GLU A 89 CPT A 504 SITE 2 AC6 10 GOL A 514 HOH A 720 HOH A 732 HOH A 850 SITE 3 AC6 10 HOH A 900 HOH A 946 SITE 1 AC7 7 LYS A 97 THR A 192 CYS A 193 PRO A 194 SITE 2 AC7 7 HOH A 874 HOH A 972 HOH A 984 SITE 1 AC8 1 LYS A 137 SITE 1 AC9 9 ARG A 82 PRO A 83 THR A 150 HOH A 605 SITE 2 AC9 9 HOH A 703 HOH A 814 HOH A 821 HOH A 973 SITE 3 AC9 9 HOH A1004 SITE 1 AD1 6 GLU A 42 73M A 503 HOH A 625 HOH A 654 SITE 2 AD1 6 HOH A 752 HOH A 947 SITE 1 AD2 2 ASP A 55 LYS A 67 SITE 1 AD3 2 LYS A 139 HOH A 858 SITE 1 AD4 4 LYS A 19 ASP A 21 HOH A 606 HOH A 784 SITE 1 AD5 7 GLU A 89 ILE A 105 PHE A 181 VAL A 184 SITE 2 AD5 7 CPT A 506 HOH A 604 HOH A 963 CRYST1 57.837 57.837 150.159 90.00 90.00 90.00 P 41 21 2 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 0.017290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006660 0.00000