HEADER SIGNALING PROTEIN 22-MAY-19 6RT2 TITLE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI PEX14 N-TERMINAL DOMAIN IN TITLE 2 COMPLEX WITH SMALL MOLECULES DESIGNED TO INVESTIGATE THE WATER TITLE 3 ENVELOPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIN 14; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI; SOURCE 3 ORGANISM_TAXID: 5702; SOURCE 4 GENE: PEX14; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PEROXISOMAL TRANSLOCATION, PPI INHIBITION, PROTEIN-INHIBITOR COMPLEX, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.NAPOLITANO,E.L.RATKOVA,M.DAWIDOWSKI,G.DUBIN,R.FINO,G.POPOWICZ, AUTHOR 2 M.SATTLER,I.V.TETKO REVDAT 3 24-JAN-24 6RT2 1 REMARK REVDAT 2 29-APR-20 6RT2 1 JRNL REVDAT 1 08-APR-20 6RT2 0 JRNL AUTH E.L.RATKOVA,M.DAWIDOWSKI,V.NAPOLITANO,G.DUBIN,R.FINO, JRNL AUTH 2 M.S.OSTERTAG,M.SATTLER,G.POPOWICZ,I.V.TETKO JRNL TITL WATER ENVELOPE HAS A CRITICAL IMPACT ON THE DESIGN OF JRNL TITL 2 PROTEIN-PROTEIN INTERACTION INHIBITORS. JRNL REF CHEM.COMMUN.(CAMB.) V. 56 4360 2020 JRNL REFN ESSN 1364-548X JRNL PMID 32195483 JRNL DOI 10.1039/C9CC07714F REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 71864 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 3575 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5329 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2076 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 202 REMARK 3 SOLVENT ATOMS : 491 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 1.06000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.71000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.723 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 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): 2599 ; 0.037 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2595 ; 0.022 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3540 ; 3.125 ; 2.065 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6038 ; 3.118 ; 3.018 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 334 ; 4.977 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;32.819 ;22.294 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 523 ;14.127 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;19.632 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 384 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2828 ; 0.018 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 595 ; 0.011 ; 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): 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 4 65 B 4 65 7828 0.130 0.050 REMARK 3 2 A 4 65 C 4 65 7848 0.150 0.050 REMARK 3 3 A 4 66 D 4 66 7864 0.160 0.050 REMARK 3 4 B 0 66 C 0 66 8366 0.140 0.050 REMARK 3 5 B 4 65 D 4 65 7748 0.160 0.050 REMARK 3 6 C 4 65 D 4 65 7886 0.130 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 : A 4 A 66 REMARK 3 ORIGIN FOR THE GROUP (A): 35.6850 -3.8666 18.0947 REMARK 3 T TENSOR REMARK 3 T11: 0.0691 T22: 0.0374 REMARK 3 T33: 0.0123 T12: 0.0071 REMARK 3 T13: -0.0120 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.2865 L22: 0.5664 REMARK 3 L33: 0.8112 L12: 0.0942 REMARK 3 L13: 0.0296 L23: 0.3943 REMARK 3 S TENSOR REMARK 3 S11: 0.0961 S12: -0.1078 S13: -0.0119 REMARK 3 S21: -0.0798 S22: -0.0825 S23: 0.0479 REMARK 3 S31: 0.0587 S32: -0.0214 S33: -0.0136 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 : B 0 B 66 REMARK 3 ORIGIN FOR THE GROUP (A): 31.1674 21.0649 22.5722 REMARK 3 T TENSOR REMARK 3 T11: 0.0183 T22: 0.0469 REMARK 3 T33: 0.0474 T12: 0.0134 REMARK 3 T13: -0.0183 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.1982 L22: 1.1002 REMARK 3 L33: 1.2665 L12: 0.4029 REMARK 3 L13: -0.4626 L23: 0.2367 REMARK 3 S TENSOR REMARK 3 S11: -0.1045 S12: -0.1069 S13: 0.0432 REMARK 3 S21: -0.1206 S22: -0.0076 S23: 0.1050 REMARK 3 S31: -0.0276 S32: -0.0404 S33: 0.1122 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 : C 0 C 66 REMARK 3 ORIGIN FOR THE GROUP (A): 50.2362 24.3878 37.0779 REMARK 3 T TENSOR REMARK 3 T11: 0.0180 T22: 0.0483 REMARK 3 T33: 0.0475 T12: -0.0083 REMARK 3 T13: -0.0062 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.7121 L22: 1.3201 REMARK 3 L33: 1.0740 L12: -0.3069 REMARK 3 L13: 0.5789 L23: 0.1767 REMARK 3 S TENSOR REMARK 3 S11: 0.0353 S12: 0.0127 S13: -0.0585 REMARK 3 S21: 0.0974 S22: 0.0296 S23: -0.0340 REMARK 3 S31: 0.0451 S32: -0.0093 S33: -0.0649 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 4 D 66 REMARK 3 ORIGIN FOR THE GROUP (A): 43.8702 -6.8793 39.7386 REMARK 3 T TENSOR REMARK 3 T11: 0.0908 T22: 0.0350 REMARK 3 T33: 0.0178 T12: -0.0232 REMARK 3 T13: -0.0062 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 0.5200 L22: 1.2921 REMARK 3 L33: 2.0091 L12: -0.3987 REMARK 3 L13: 0.2228 L23: -0.1169 REMARK 3 S TENSOR REMARK 3 S11: -0.0044 S12: -0.0034 S13: 0.0013 REMARK 3 S21: 0.0074 S22: -0.0540 S23: -0.0369 REMARK 3 S31: -0.3036 S32: 0.0557 S33: 0.0584 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6RT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-17 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, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 145521 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 2.512 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.41 REMARK 200 R MERGE FOR SHELL (I) : 0.46800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.810 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: 5AON REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA2SO4, 0.1 M BIS-TRIS PROPANE PH REMARK 280 7.5, 20% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 57.76000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 0 REMARK 465 TRP A 1 REMARK 465 HIS A 2 REMARK 465 THR A 3 REMARK 465 MET D 0 REMARK 465 TRP D 1 REMARK 465 HIS D 2 REMARK 465 THR D 3 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 HIS A 4 CG ND1 CD2 CE1 NE2 REMARK 470 MET B 0 CG SD CE REMARK 470 HIS B 2 CG ND1 CD2 CE1 NE2 REMARK 470 MET C 0 CG SD CE REMARK 470 GLU D 6 CD OE1 OE2 REMARK 470 LYS D 9 CD CE NZ 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 OE2 GLU D 60 O HOH D 202 1.59 REMARK 500 NH1 ARG A 22 O HOH A 201 2.03 REMARK 500 O ARG D 22 O HOH D 203 2.04 REMARK 500 OE1 GLU B 16 O HOH B 201 2.06 REMARK 500 NH1 ARG C 25 O HOH C 201 2.07 REMARK 500 O LEU D 19 NH1 ARG D 24 2.18 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 7 NE ARG A 7 CZ -0.086 REMARK 500 GLN A 54 CG GLN A 54 CD 0.161 REMARK 500 GLU A 60 CD GLU A 60 OE2 0.072 REMARK 500 ARG B 22 CZ ARG B 22 NH1 0.081 REMARK 500 GLU B 60 CD GLU B 60 OE2 0.068 REMARK 500 GLU C 16 CD GLU C 16 OE1 0.100 REMARK 500 GLU C 47 CD GLU C 47 OE2 0.079 REMARK 500 GLU C 60 CD GLU C 60 OE1 0.086 REMARK 500 GLU D 16 CB GLU D 16 CG 0.180 REMARK 500 GLU D 16 CG GLU D 16 CD 0.128 REMARK 500 GLU D 16 CD GLU D 16 OE2 0.117 REMARK 500 GLU D 60 CG GLU D 60 CD 0.107 REMARK 500 GLU D 60 CD GLU D 60 OE1 0.087 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 GLU A 6 OE1 - CD - OE2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 7 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLU A 16 OE1 - CD - OE2 ANGL. DEV. = -9.5 DEGREES REMARK 500 ASP A 20 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 LYS A 38 O - C - N ANGL. DEV. = -12.4 DEGREES REMARK 500 ARG A 63 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 63 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG B 7 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 7 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG B 10 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP B 20 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG B 22 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 24 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 LYS B 36 CD - CE - NZ ANGL. DEV. = -33.4 DEGREES REMARK 500 ARG B 63 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 63 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 GLU C 16 CG - CD - OE2 ANGL. DEV. = -13.8 DEGREES REMARK 500 ARG C 22 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG C 63 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG C 63 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG D 7 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 GLU D 16 OE1 - CD - OE2 ANGL. DEV. = -7.7 DEGREES REMARK 500 GLU D 16 CG - CD - OE1 ANGL. DEV. = -12.4 DEGREES REMARK 500 GLU D 16 CG - CD - OE2 ANGL. DEV. = 12.6 DEGREES REMARK 500 ASP D 20 OD1 - CG - OD2 ANGL. DEV. = 12.6 DEGREES REMARK 500 ASP D 20 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP D 20 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG D 22 CG - CD - NE ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG D 22 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES 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 SER D 21 -14.21 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 A 327 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH D 319 DISTANCE = 5.84 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CV5 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CV5 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CV5 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CV5 D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BME B 105 and CYS B REMARK 800 46 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BME C 102 and CYS C REMARK 800 46 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BME D 104 and CYS D REMARK 800 46 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OML RELATED DB: PDB REMARK 900 5=ML CONTAIN THE SAME PROTEIN COMPLEXED WITH A DIFFERENT INHIBITOR DBREF 6RT2 A 2 66 UNP Q8IEW2 Q8IEW2_TRYBB 20 84 DBREF 6RT2 B 2 66 UNP Q8IEW2 Q8IEW2_TRYBB 20 84 DBREF 6RT2 C 2 66 UNP Q8IEW2 Q8IEW2_TRYBB 20 84 DBREF 6RT2 D 2 66 UNP Q8IEW2 Q8IEW2_TRYBB 20 84 SEQADV 6RT2 MET A 0 UNP Q8IEW2 INITIATING METHIONINE SEQADV 6RT2 TRP A 1 UNP Q8IEW2 EXPRESSION TAG SEQADV 6RT2 MET B 0 UNP Q8IEW2 INITIATING METHIONINE SEQADV 6RT2 TRP B 1 UNP Q8IEW2 EXPRESSION TAG SEQADV 6RT2 MET C 0 UNP Q8IEW2 INITIATING METHIONINE SEQADV 6RT2 TRP C 1 UNP Q8IEW2 EXPRESSION TAG SEQADV 6RT2 MET D 0 UNP Q8IEW2 INITIATING METHIONINE SEQADV 6RT2 TRP D 1 UNP Q8IEW2 EXPRESSION TAG SEQRES 1 A 67 MET TRP HIS THR HIS SER GLU ARG GLU LYS ARG VAL SER SEQRES 2 A 67 ASN ALA VAL GLU PHE LEU LEU ASP SER ARG VAL ARG ARG SEQRES 3 A 67 THR PRO THR SER SER LYS VAL HIS PHE LEU LYS SER LYS SEQRES 4 A 67 GLY LEU SER ALA GLU GLU ILE CYS GLU ALA PHE THR LYS SEQRES 5 A 67 VAL GLY GLN PRO LYS THR LEU ASN GLU ILE LYS ARG ILE SEQRES 6 A 67 LEU SER SEQRES 1 B 67 MET TRP HIS THR HIS SER GLU ARG GLU LYS ARG VAL SER SEQRES 2 B 67 ASN ALA VAL GLU PHE LEU LEU ASP SER ARG VAL ARG ARG SEQRES 3 B 67 THR PRO THR SER SER LYS VAL HIS PHE LEU LYS SER LYS SEQRES 4 B 67 GLY LEU SER ALA GLU GLU ILE CYS GLU ALA PHE THR LYS SEQRES 5 B 67 VAL GLY GLN PRO LYS THR LEU ASN GLU ILE LYS ARG ILE SEQRES 6 B 67 LEU SER SEQRES 1 C 67 MET TRP HIS THR HIS SER GLU ARG GLU LYS ARG VAL SER SEQRES 2 C 67 ASN ALA VAL GLU PHE LEU LEU ASP SER ARG VAL ARG ARG SEQRES 3 C 67 THR PRO THR SER SER LYS VAL HIS PHE LEU LYS SER LYS SEQRES 4 C 67 GLY LEU SER ALA GLU GLU ILE CYS GLU ALA PHE THR LYS SEQRES 5 C 67 VAL GLY GLN PRO LYS THR LEU ASN GLU ILE LYS ARG ILE SEQRES 6 C 67 LEU SER SEQRES 1 D 67 MET TRP HIS THR HIS SER GLU ARG GLU LYS ARG VAL SER SEQRES 2 D 67 ASN ALA VAL GLU PHE LEU LEU ASP SER ARG VAL ARG ARG SEQRES 3 D 67 THR PRO THR SER SER LYS VAL HIS PHE LEU LYS SER LYS SEQRES 4 D 67 GLY LEU SER ALA GLU GLU ILE CYS GLU ALA PHE THR LYS SEQRES 5 D 67 VAL GLY GLN PRO LYS THR LEU ASN GLU ILE LYS ARG ILE SEQRES 6 D 67 LEU SER HET CV5 A 101 39 HET SO4 A 102 5 HET BME A 103 4 HET CV5 B 101 39 HET SO4 B 102 5 HET SO4 B 103 5 HET SO4 B 104 5 HET BME B 105 4 HET CV5 C 101 39 HET BME C 102 4 HET CV5 D 101 39 HET SO4 D 102 5 HET SO4 D 103 5 HET BME D 104 4 HETNAM CV5 (3~{S})-3-[[1-(2-HYDROXYETHYL)-5-[(4-METHOXYNAPHTHALEN- HETNAM 2 CV5 1-YL)METHYL]-6,7-DIHYDRO-4~{H}-PYRAZOLO[4,3-C]PYRIDIN- HETNAM 3 CV5 3-YL]CARBONYLAMINO]-3-PHENYL-PROPANOIC ACID HETNAM SO4 SULFATE ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 5 CV5 4(C30 H32 N4 O5) FORMUL 6 SO4 6(O4 S 2-) FORMUL 7 BME 4(C2 H6 O S) FORMUL 19 HOH *491(H2 O) HELIX 1 AA1 SER A 5 ASP A 20 1 16 HELIX 2 AA2 ASP A 20 ARG A 25 1 6 HELIX 3 AA3 PRO A 27 LYS A 38 1 12 HELIX 4 AA4 SER A 41 VAL A 52 1 12 HELIX 5 AA5 THR A 57 SER A 66 1 10 HELIX 6 AA6 MET B 0 HIS B 4 5 5 HELIX 7 AA7 SER B 5 ASP B 20 1 16 HELIX 8 AA8 ASP B 20 THR B 26 1 7 HELIX 9 AA9 PRO B 27 LYS B 38 1 12 HELIX 10 AB1 SER B 41 VAL B 52 1 12 HELIX 11 AB2 THR B 57 SER B 66 1 10 HELIX 12 AB3 MET C 0 HIS C 4 5 5 HELIX 13 AB4 SER C 5 ASP C 20 1 16 HELIX 14 AB5 ASP C 20 ARG C 25 1 6 HELIX 15 AB6 PRO C 27 LYS C 38 1 12 HELIX 16 AB7 SER C 41 VAL C 52 1 12 HELIX 17 AB8 THR C 57 SER C 66 1 10 HELIX 18 AB9 SER D 5 ASP D 20 1 16 HELIX 19 AC1 ASP D 20 ARG D 25 1 6 HELIX 20 AC2 PRO D 27 LYS D 38 1 12 HELIX 21 AC3 SER D 41 VAL D 52 1 12 HELIX 22 AC4 THR D 57 SER D 66 1 10 LINK SG CYS A 46 S2 BME A 103 1555 1555 1.92 LINK SG CYS B 46 S2 BME B 105 1555 1555 1.99 LINK SG CYS C 46 S2 BME C 102 1555 1555 2.03 LINK SG CYS D 46 S2 BME D 104 1555 1555 2.05 SITE 1 AC1 17 ASN A 13 ALA A 14 GLU A 16 PHE A 17 SITE 2 AC1 17 ARG A 22 THR A 26 PHE A 34 LEU A 35 SITE 3 AC1 17 LYS A 38 HOH A 206 HOH A 239 HOH A 242 SITE 4 AC1 17 HOH A 251 HOH A 263 SER D 30 HIS D 33 SITE 5 AC1 17 CV5 D 101 SITE 1 AC2 10 SER A 41 ALA A 42 HOH A 208 HOH A 226 SITE 2 AC2 10 HOH A 231 HOH A 264 HOH A 275 SER B 5 SITE 3 AC2 10 GLU B 6 HOH B 283 SITE 1 AC3 4 GLU A 43 CYS A 46 GLU A 47 HOH D 249 SITE 1 AC4 15 ASN B 13 GLU B 16 PHE B 17 ARG B 22 SITE 2 AC4 15 VAL B 23 THR B 26 SER B 30 PHE B 34 SITE 3 AC4 15 LEU B 35 LYS B 38 HOH B 226 HOH B 273 SITE 4 AC4 15 HOH B 281 HIS C 33 CV5 C 101 SITE 1 AC5 10 SER A 5 GLU A 6 LYS B 36 SER B 41 SITE 2 AC5 10 ALA B 42 HOH B 213 HOH B 230 HOH B 271 SITE 3 AC5 10 HOH B 287 HOH B 289 SITE 1 AC6 5 PRO B 27 THR B 28 LYS B 56 HOH B 225 SITE 2 AC6 5 HOH B 227 SITE 1 AC7 6 THR B 57 ASN B 59 ARG B 63 HOH B 251 SITE 2 AC7 6 HOH B 256 BME C 102 SITE 1 AC8 15 PHE B 34 SER B 37 CV5 B 101 ASN C 13 SITE 2 AC8 15 ALA C 14 PHE C 17 THR C 26 PHE C 34 SITE 3 AC8 15 LEU C 35 LYS C 38 HOH C 215 HOH C 224 SITE 4 AC8 15 HOH C 229 HOH C 244 HOH C 268 SITE 1 AC9 17 PHE A 34 SER A 37 CV5 A 101 ASN D 13 SITE 2 AC9 17 ALA D 14 PHE D 17 ARG D 22 THR D 26 SITE 3 AC9 17 SER D 30 PHE D 34 LEU D 35 LYS D 38 SITE 4 AC9 17 LEU D 40 HOH D 208 HOH D 226 HOH D 244 SITE 5 AC9 17 HOH D 259 SITE 1 AD1 6 PRO D 27 THR D 28 SER D 29 HOH D 205 SITE 2 AD1 6 HOH D 216 HOH D 256 SITE 1 AD2 6 THR D 57 ASN D 59 ARG D 63 HOH D 207 SITE 2 AD2 6 HOH D 227 HOH D 260 SITE 1 AD3 15 ALA B 42 GLU B 43 GLU B 44 ILE B 45 SITE 2 AD3 15 GLU B 47 ALA B 48 PHE B 49 THR B 50 SITE 3 AD3 15 LYS B 56 ILE B 61 HOH B 208 HOH B 211 SITE 4 AD3 15 HOH B 215 ARG C 7 HOH C 203 SITE 1 AD4 14 SO4 B 104 ALA C 42 GLU C 43 GLU C 44 SITE 2 AD4 14 ILE C 45 GLU C 47 ALA C 48 PHE C 49 SITE 3 AD4 14 THR C 50 LYS C 56 LEU C 58 ILE C 61 SITE 4 AD4 14 HOH C 209 HOH C 220 SITE 1 AD5 15 ASN A 59 ALA D 42 GLU D 43 GLU D 44 SITE 2 AD5 15 ILE D 45 GLU D 47 ALA D 48 PHE D 49 SITE 3 AD5 15 THR D 50 LYS D 56 LEU D 58 ILE D 61 SITE 4 AD5 15 HOH D 224 HOH D 241 HOH D 284 CRYST1 35.780 115.520 38.870 90.00 101.39 90.00 P 1 21 1 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 0.027949 0.000000 0.005628 0.00000 SCALE2 0.000000 0.008657 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026243 0.00000