HEADER HYDROLASE 02-DEC-18 6IC7 TITLE HUMAN CATHEPSIN-C IN COMPLEX WITH DIPEPTIDYL CYCLOPROPYL NITRILE TITLE 2 INHIBITOR 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPEPTIDYL PEPTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CATHEPSIN C,CATHEPSIN J,DIPEPTIDYL PEPTIDASE I,DPPI, COMPND 5 DIPEPTIDYL TRANSFERASE; COMPND 6 EC: 3.4.14.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DIPEPTIDYL PEPTIDASE 1; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: CATHEPSIN C,CATHEPSIN J,DIPEPTIDYL PEPTIDASE I,DPPI, COMPND 12 DIPEPTIDYL TRANSFERASE; COMPND 13 EC: 3.4.14.1; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DIPEPTIDYL PEPTIDASE 1; COMPND 17 CHAIN: C; COMPND 18 SYNONYM: CATHEPSIN C,CATHEPSIN J,DIPEPTIDYL PEPTIDASE I,DPPI, COMPND 19 DIPEPTIDYL TRANSFERASE; COMPND 20 EC: 3.4.14.1; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CTSC, CPPI; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: BTI-TN-5B1-4; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: CTSC, CPPI; SOURCE 14 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: BTI-TN-5B1-4; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 GENE: CTSC, CPPI; SOURCE 22 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 24 EXPRESSION_SYSTEM_CELL_LINE: BTI-TN-5B1-4 KEYWDS CATHEPSIN-C, CYSTEINE PROTEASE, STRUCTURE-BASED DRUG DESIGN, KEYWDS 2 ARTHRITIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.HAKANSSON,D.T.LOGAN,B.KORKMAZ,A.LESNER,M.WYSOCKA,A.GIELDON, AUTHOR 2 F.GAUTHIER,D.JENNE,C.LAURITZEN,J.PEDERSEN REVDAT 4 13-NOV-24 6IC7 1 HETSYN LINK REVDAT 3 29-JUL-20 6IC7 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 ATOM REVDAT 2 22-MAY-19 6IC7 1 JRNL REVDAT 1 24-APR-19 6IC7 0 JRNL AUTH B.KORKMAZ,A.LESNER,M.WYSOCKA,A.GIELDON,M.HAKANSSON, JRNL AUTH 2 F.GAUTHIER,D.T.LOGAN,D.E.JENNE,C.LAURITZEN,J.PEDERSEN JRNL TITL STRUCTURE-BASED DESIGN AND IN VIVO ANTI-ARTHRITIC ACTIVITY JRNL TITL 2 EVALUATION OF A POTENT DIPEPTIDYL CYCLOPROPYL NITRILE JRNL TITL 3 INHIBITOR OF CATHEPSIN C. JRNL REF BIOCHEM. PHARMACOL. V. 164 349 2019 JRNL REFN ISSN 1873-2968 JRNL PMID 30978322 JRNL DOI 10.1016/J.BCP.2019.04.006 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 2018/15/10 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 29338 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1466 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1741 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.2020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2758 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 127 REMARK 3 SOLVENT ATOMS : 349 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14600 REMARK 3 B22 (A**2) : 0.41700 REMARK 3 B33 (A**2) : -0.56300 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): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.767 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3061 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2619 ; 0.002 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4195 ; 1.931 ; 1.709 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6113 ; 1.462 ; 1.633 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 376 ;19.050 ; 5.346 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;29.536 ;22.933 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 436 ;14.674 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;23.757 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 403 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3705 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 691 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 634 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 67 ; 0.216 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1489 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 297 ; 0.212 ; 0.200 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): 1424 ; 1.396 ; 1.401 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1423 ; 1.395 ; 1.400 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1786 ; 2.349 ; 2.092 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1787 ; 2.349 ; 2.093 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1637 ; 1.358 ; 1.574 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1638 ; 1.358 ; 1.575 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2401 ; 2.225 ; 2.318 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2402 ; 2.225 ; 2.319 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): -6.8400 -25.2890 -20.1850 REMARK 3 T TENSOR REMARK 3 T11: 0.0337 T22: 0.0214 REMARK 3 T33: 0.0446 T12: 0.0198 REMARK 3 T13: 0.0013 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 1.6197 L22: 1.2551 REMARK 3 L33: 1.2324 L12: -0.0383 REMARK 3 L13: 0.4764 L23: 0.1648 REMARK 3 S TENSOR REMARK 3 S11: -0.0107 S12: 0.0025 S13: 0.0879 REMARK 3 S21: -0.0938 S22: -0.0211 S23: 0.1128 REMARK 3 S31: -0.1275 S32: -0.1008 S33: 0.0318 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 206 B 367 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6010 -30.7790 -17.9780 REMARK 3 T TENSOR REMARK 3 T11: 0.0049 T22: 0.0298 REMARK 3 T33: 0.0357 T12: -0.0086 REMARK 3 T13: 0.0006 T23: 0.0161 REMARK 3 L TENSOR REMARK 3 L11: 1.1303 L22: 1.2679 REMARK 3 L33: 0.8449 L12: 0.0273 REMARK 3 L13: -0.0689 L23: 0.2074 REMARK 3 S TENSOR REMARK 3 S11: -0.0148 S12: -0.0109 S13: -0.0433 REMARK 3 S21: -0.0044 S22: 0.0004 S23: -0.1286 REMARK 3 S31: -0.0478 S32: 0.1379 S33: 0.0145 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 372 C 439 REMARK 3 ORIGIN FOR THE GROUP (A): 20.2390 -24.4060 -8.8540 REMARK 3 T TENSOR REMARK 3 T11: 0.0792 T22: 0.1131 REMARK 3 T33: 0.0707 T12: -0.0386 REMARK 3 T13: -0.0191 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 0.9605 L22: 1.2573 REMARK 3 L33: 1.1713 L12: 0.0522 REMARK 3 L13: -0.1637 L23: 0.3884 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: -0.1569 S13: 0.0732 REMARK 3 S21: 0.1278 S22: 0.0034 S23: -0.1607 REMARK 3 S31: -0.1228 S32: 0.2362 S33: -0.0223 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6IC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013204. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : BRUKER X8 PROTEUM 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 : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM REMARK 200 DATA SCALING SOFTWARE : PROTEUM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.16400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.0 % (W/V) PEG 3000 0.2 M AMMONIUM REMARK 280 CITRATE DIBASIC 2.5 MM DTT, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 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 0.00000 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 43.68250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.77450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.50200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.68250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.77450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.50200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.68250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.77450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.50200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.68250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.77450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.50200 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: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 51750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -227.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -87.54900 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -87.54900 REMARK 350 BIOMT3 4 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 GLY A 119 REMARK 465 ASP C 371 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 HOH B 605 O HOH C 512 1.73 REMARK 500 O HOH B 606 O HOH B 641 1.94 REMARK 500 O HOH B 557 O HOH B 629 1.97 REMARK 500 O HOH A 729 O HOH A 730 2.07 REMARK 500 O HOH A 719 O HOH A 758 2.07 REMARK 500 OD2 ASP A 52 ND2 ASN A 73 2.08 REMARK 500 O HOH C 506 O HOH C 518 2.12 REMARK 500 SG CYS B 234 C36 H9H B 403 2.17 REMARK 500 O HOH C 506 O HOH C 533 2.19 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 794 O HOH B 605 3555 1.71 REMARK 500 O HOH A 801 O HOH B 622 8444 2.12 REMARK 500 O HOH A 796 O HOH C 561 2545 2.14 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 GLY A 20 C GLY A 20 O 0.127 REMARK 500 GLU B 294 CD GLU B 294 OE1 -0.100 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 CYS A 30 CB - CA - C ANGL. DEV. = 11.9 DEGREES REMARK 500 ARG B 315 NE - CZ - NH1 ANGL. DEV. = 4.0 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 SER A 21 30.77 79.56 REMARK 500 MET A 33 98.54 -67.42 REMARK 500 ASP A 48 26.84 -153.01 REMARK 500 TYR A 64 -120.67 48.41 REMARK 500 ASN B 215 80.00 -151.67 REMARK 500 ALA B 229 -150.91 61.25 REMARK 500 SER B 230 47.23 -89.84 REMARK 500 PHE B 298 80.81 -150.28 REMARK 500 PHE C 373 108.38 -56.87 REMARK 500 ASN C 380 -2.99 -146.41 REMARK 500 SER C 392 -70.26 -41.55 REMARK 500 ILE C 429 46.38 -151.81 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 PRO C 375 PHE C 376 149.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6IC5 RELATED DB: PDB REMARK 900 RELATED ID: 6IC6 RELATED DB: PDB DBREF 6IC7 A 1 119 UNP P53634 CATC_HUMAN 25 143 DBREF 6IC7 B 206 367 UNP P53634 CATC_HUMAN 230 391 DBREF 6IC7 C 371 439 UNP P53634 CATC_HUMAN 395 463 SEQRES 1 A 119 ASP THR PRO ALA ASN CYS THR TYR LEU ASP LEU LEU GLY SEQRES 2 A 119 THR TRP VAL PHE GLN VAL GLY SER SER GLY SER GLN ARG SEQRES 3 A 119 ASP VAL ASN CYS SER VAL MET GLY PRO GLN GLU LYS LYS SEQRES 4 A 119 VAL VAL VAL TYR LEU GLN LYS LEU ASP THR ALA TYR ASP SEQRES 5 A 119 ASP LEU GLY ASN SER GLY HIS PHE THR ILE ILE TYR ASN SEQRES 6 A 119 GLN GLY PHE GLU ILE VAL LEU ASN ASP TYR LYS TRP PHE SEQRES 7 A 119 ALA PHE PHE LYS TYR LYS GLU GLU GLY SER LYS VAL THR SEQRES 8 A 119 THR TYR CYS ASN GLU THR MET THR GLY TRP VAL HIS ASP SEQRES 9 A 119 VAL LEU GLY ARG ASN TRP ALA CYS PHE THR GLY LYS LYS SEQRES 10 A 119 VAL GLY SEQRES 1 B 162 HIS LEU PRO THR SER TRP ASP TRP ARG ASN VAL HIS GLY SEQRES 2 B 162 ILE ASN PHE VAL SER PRO VAL ARG ASN GLN ALA SER CYS SEQRES 3 B 162 GLY SER CYS TYR SER PHE ALA SER MET GLY MET LEU GLU SEQRES 4 B 162 ALA ARG ILE ARG ILE LEU THR ASN ASN SER GLN THR PRO SEQRES 5 B 162 ILE LEU SER PRO GLN GLU VAL VAL SER CYS SER GLN TYR SEQRES 6 B 162 ALA GLN GLY CYS GLU GLY GLY PHE PRO TYR LEU ILE ALA SEQRES 7 B 162 GLY LYS TYR ALA GLN ASP PHE GLY LEU VAL GLU GLU ALA SEQRES 8 B 162 CYS PHE PRO TYR THR GLY THR ASP SER PRO CYS LYS MET SEQRES 9 B 162 LYS GLU ASP CYS PHE ARG TYR TYR SER SER GLU TYR HIS SEQRES 10 B 162 TYR VAL GLY GLY PHE TYR GLY GLY CYS ASN GLU ALA LEU SEQRES 11 B 162 MET LYS LEU GLU LEU VAL HIS HIS GLY PRO MET ALA VAL SEQRES 12 B 162 ALA PHE GLU VAL TYR ASP ASP PHE LEU HIS TYR LYS LYS SEQRES 13 B 162 GLY ILE TYR HIS HIS THR SEQRES 1 C 69 ASP PRO PHE ASN PRO PHE GLU LEU THR ASN HIS ALA VAL SEQRES 2 C 69 LEU LEU VAL GLY TYR GLY THR ASP SER ALA SER GLY MET SEQRES 3 C 69 ASP TYR TRP ILE VAL LYS ASN SER TRP GLY THR GLY TRP SEQRES 4 C 69 GLY GLU ASN GLY TYR PHE ARG ILE ARG ARG GLY THR ASP SEQRES 5 C 69 GLU CYS ALA ILE GLU SER ILE ALA VAL ALA ALA THR PRO SEQRES 6 C 69 ILE PRO LYS LEU HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET MAN D 4 11 HET MAN D 5 11 HET NAG A 601 14 HET NAG B 401 14 HET CL B 402 1 HET H9H B 403 37 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM CL CHLORIDE ION HETNAM H9H 1-AZANYL-~{N}-[(1~{R},2~{R})-1-CYANO-2-[4-[4-(4- HETNAM 2 H9H METHYLPIPERAZIN-1-YL) HETNAM 3 H9H SULFONYLPHENYL]PHENYL]CYCLOPROPYL]CYCLOHEXANE-1- HETNAM 4 H9H CARBOXAMIDE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 4 NAG 4(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 4 MAN 2(C6 H12 O6) FORMUL 7 CL CL 1- FORMUL 8 H9H C28 H35 N5 O3 S FORMUL 9 HOH *349(H2 O) HELIX 1 AA1 THR A 7 LEU A 12 1 6 HELIX 2 AA2 ASN A 29 MET A 33 5 5 HELIX 3 AA3 SER B 233 THR B 251 1 19 HELIX 4 AA4 SER B 260 SER B 268 1 9 HELIX 5 AA5 GLN B 272 GLY B 276 5 5 HELIX 6 AA6 PHE B 278 ALA B 283 1 6 HELIX 7 AA7 GLY B 284 PHE B 290 1 7 HELIX 8 AA8 GLU B 294 PHE B 298 5 5 HELIX 9 AA9 ASN B 332 GLY B 344 1 13 HELIX 10 AB1 TYR B 353 HIS B 358 1 6 HELIX 11 AB2 ASP C 422 ILE C 426 5 5 SHEET 1 AA112 TYR A 75 GLU A 86 0 SHEET 2 AA112 LYS A 89 THR A 97 -1 O THR A 91 N LYS A 84 SHEET 3 AA112 TRP A 110 LYS A 117 -1 O LYS A 117 N ASN A 95 SHEET 4 AA112 TYR A 75 GLU A 86 0 SHEET 5 AA112 GLY A 67 LEU A 72 -1 N ILE A 70 O TRP A 77 SHEET 6 AA112 SER A 57 ILE A 63 -1 N HIS A 59 O VAL A 71 SHEET 7 AA112 THR A 49 ASP A 52 -1 N ALA A 50 O GLY A 58 SHEET 8 AA112 LYS A 38 GLN A 45 -1 N TYR A 43 O TYR A 51 SHEET 9 AA112 GLY A 13 SER A 24 -1 N VAL A 19 O LYS A 38 SHEET 10 AA112 TRP A 110 LYS A 117 -1 O CYS A 112 N GLY A 20 SHEET 11 AA112 GLY A 100 ASP A 104 -1 N GLY A 100 O PHE A 113 SHEET 12 AA112 TRP A 110 LYS A 117 -1 O PHE A 113 N GLY A 100 SHEET 1 AA2 3 TRP B 211 ASP B 212 0 SHEET 2 AA2 3 HIS C 381 THR C 390 -1 O TYR C 388 N TRP B 211 SHEET 3 AA2 3 MET B 346 PHE B 350 -1 N MET B 346 O LEU C 385 SHEET 1 AA3 5 TRP B 211 ASP B 212 0 SHEET 2 AA3 5 HIS C 381 THR C 390 -1 O TYR C 388 N TRP B 211 SHEET 3 AA3 5 ASP C 397 LYS C 402 -1 O LYS C 402 N LEU C 384 SHEET 4 AA3 5 TYR C 414 ARG C 418 -1 O PHE C 415 N VAL C 401 SHEET 5 AA3 5 ILE B 363 TYR B 364 1 N TYR B 364 O ARG C 416 SHEET 1 AA4 2 SER B 318 TYR B 323 0 SHEET 2 AA4 2 VAL C 431 PRO C 435 -1 O ALA C 432 N HIS B 322 SSBOND 1 CYS A 6 CYS A 94 1555 1555 2.05 SSBOND 2 CYS A 30 CYS A 112 1555 1555 2.04 SSBOND 3 CYS B 231 CYS B 274 1555 1555 2.02 SSBOND 4 CYS B 267 CYS B 307 1555 1555 2.00 SSBOND 5 CYS B 297 CYS B 313 1555 1555 2.06 LINK ND2 ASN A 5 C1 NAG A 601 1555 1555 1.45 LINK ND2 ASN A 95 C1 NAG D 1 1555 1555 1.43 LINK ND2 ASN B 252 C1 NAG B 401 1555 1555 1.42 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.43 LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.44 LINK O2 MAN D 4 C1 MAN D 5 1555 1555 1.42 CISPEP 1 LYS A 46 LEU A 47 0 -2.01 CRYST1 87.365 87.549 115.004 90.00 90.00 90.00 I 2 2 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 0.011446 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011422 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008695 0.00000