HEADER HYDROLASE 26-NOV-04 1Y3U TITLE TRYPSIN INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN, CATIONIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-TRYPSIN, FRAGMENT; COMPND 5 EC: 3.4.21.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 TISSUE: BLOOD KEYWDS TRYPSIN, INHIBITOR COMPLEX, BARREL, 6 STRANDED BETA-SHEET, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.FOKKENS,U.OBST,A.HEINE,F.DIEDERICH,G.KLEBE REVDAT 5 20-NOV-24 1Y3U 1 REMARK REVDAT 4 23-AUG-23 1Y3U 1 REMARK LINK REVDAT 3 11-OCT-17 1Y3U 1 REMARK REVDAT 2 24-FEB-09 1Y3U 1 VERSN REVDAT 1 06-DEC-05 1Y3U 0 JRNL AUTH J.FOKKENS,U.OBST-SANDER,A.HEINE,F.DIEDERICH,G.KLEBE JRNL TITL STRUCTURAL AND THERMODYNAMIC CHARACTERISATION OF JRNL TITL 2 PROTEIN-INHIBITOR-COMPLEXES OF THROMBIN AND TRYPSIN JRNL TITL 3 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.155 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.152 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2321 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 24193 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.148 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21444 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1756.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1552.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7112 REMARK 3 NUMBER OF RESTRAINTS : 6885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.026 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.044 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.048 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.031 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.065 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 1Y3U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000031081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-02 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 6.00 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NONE REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25191 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 10.86 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : 0.39900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.350 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: PDB ENTRY 1MTS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MES, CALCIUM REMARK 280 CHLORIDE, BENZAMIDINIUM HYDROCHLORIDE, PH 6.00, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 31.64500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.64500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.70000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 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 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 LYS A 109 CG CD CE NZ REMARK 470 LYS A 145 CG CD CE NZ REMARK 470 ASP A 165 CG OD1 OD2 REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 LYS A 239 CG CD CE NZ 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 HIS A 40 CG - ND1 - CE1 ANGL. DEV. = 7.5 DEGREES REMARK 500 HIS A 91 CG - ND1 - CE1 ANGL. DEV. = 6.0 DEGREES REMARK 500 TYR A 234 CB - CG - CD1 ANGL. DEV. = 3.7 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 71 -76.00 -123.64 REMARK 500 ASN A 79 -3.10 81.48 REMARK 500 ASN A 115 -168.50 -160.26 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 CA A3394 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE1 REMARK 620 2 ASN A 72 O 91.0 REMARK 620 3 VAL A 75 O 163.3 82.4 REMARK 620 4 GLU A 80 OE2 103.6 156.8 87.7 REMARK 620 5 HOH A3398 O 79.7 103.2 86.9 97.1 REMARK 620 6 HOH A3408 O 85.3 84.4 109.2 79.1 163.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 3394 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UIQ A 1994 DBREF 1Y3U A 16 245 UNP P00760 TRY1_BOVIN 21 243 SEQRES 1 A 223 ILE VAL GLY GLY TYR THR CYS GLY ALA ASN THR VAL PRO SEQRES 2 A 223 TYR GLN VAL SER LEU ASN SER GLY TYR HIS PHE CYS GLY SEQRES 3 A 223 GLY SER LEU ILE ASN SER GLN TRP VAL VAL SER ALA ALA SEQRES 4 A 223 HIS CYS TYR LYS SER GLY ILE GLN VAL ARG LEU GLY GLU SEQRES 5 A 223 ASP ASN ILE ASN VAL VAL GLU GLY ASN GLU GLN PHE ILE SEQRES 6 A 223 SER ALA SER LYS SER ILE VAL HIS PRO SER TYR ASN SER SEQRES 7 A 223 ASN THR LEU ASN ASN ASP ILE MET LEU ILE LYS LEU LYS SEQRES 8 A 223 SER ALA ALA SER LEU ASN SER ARG VAL ALA SER ILE SER SEQRES 9 A 223 LEU PRO THR SER CYS ALA SER ALA GLY THR GLN CYS LEU SEQRES 10 A 223 ILE SER GLY TRP GLY ASN THR LYS SER SER GLY THR SER SEQRES 11 A 223 TYR PRO ASP VAL LEU LYS CYS LEU LYS ALA PRO ILE LEU SEQRES 12 A 223 SER ASP SER SER CYS LYS SER ALA TYR PRO GLY GLN ILE SEQRES 13 A 223 THR SER ASN MET PHE CYS ALA GLY TYR LEU GLU GLY GLY SEQRES 14 A 223 LYS ASP SER CYS GLN GLY ASP SER GLY GLY PRO VAL VAL SEQRES 15 A 223 CYS SER GLY LYS LEU GLN GLY ILE VAL SER TRP GLY SER SEQRES 16 A 223 GLY CYS ALA GLN LYS ASN LYS PRO GLY VAL TYR THR LYS SEQRES 17 A 223 VAL CYS ASN TYR VAL SER TRP ILE LYS GLN THR ILE ALA SEQRES 18 A 223 SER ASN HET CA A3394 1 HET UIQ A1994 44 HETNAM CA CALCIUM ION HETNAM UIQ (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YLMETHYL-1- HETNAM 2 UIQ ISOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4- HETNAM 3 UIQ YL)-BENZAMIDINE FORMUL 2 CA CA 2+ FORMUL 3 UIQ C27 H32 N4 O3 FORMUL 4 HOH *115(H2 O) HELIX 1 1 ALA A 55 TYR A 59 5 5 HELIX 2 2 SER A 164 TYR A 172 1 9 HELIX 3 3 TYR A 234 SER A 244 1 11 SHEET 1 A 7 TYR A 20 THR A 21 0 SHEET 2 A 7 LYS A 156 PRO A 161 -1 O CYS A 157 N TYR A 20 SHEET 3 A 7 GLN A 135 GLY A 140 -1 N ILE A 138 O LEU A 158 SHEET 4 A 7 PRO A 198 CYS A 201 -1 O VAL A 200 N LEU A 137 SHEET 5 A 7 LYS A 204 TRP A 215 -1 O LYS A 204 N CYS A 201 SHEET 6 A 7 GLY A 226 LYS A 230 -1 O VAL A 227 N TRP A 215 SHEET 7 A 7 MET A 180 ALA A 183 -1 N PHE A 181 O TYR A 228 SHEET 1 B 7 GLN A 30 ASN A 34 0 SHEET 2 B 7 HIS A 40 LEU A 46 -1 O CYS A 42 N LEU A 33 SHEET 3 B 7 TRP A 51 SER A 54 -1 O VAL A 53 N SER A 45 SHEET 4 B 7 MET A 104 LEU A 108 -1 O ILE A 106 N VAL A 52 SHEET 5 B 7 GLN A 81 VAL A 90 -1 N ILE A 89 O LEU A 105 SHEET 6 B 7 GLN A 64 LEU A 67 -1 N VAL A 65 O ILE A 83 SHEET 7 B 7 GLN A 30 ASN A 34 -1 N SER A 32 O ARG A 66 SSBOND 1 CYS A 22 CYS A 157 1555 1555 2.03 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 3 CYS A 128 CYS A 232 1555 1555 2.05 SSBOND 4 CYS A 136 CYS A 201 1555 1555 2.01 SSBOND 5 CYS A 168 CYS A 182 1555 1555 2.02 SSBOND 6 CYS A 191 CYS A 220 1555 1555 2.05 LINK OE1 GLU A 70 CA CA A3394 1555 1555 2.26 LINK O ASN A 72 CA CA A3394 1555 1555 2.30 LINK O VAL A 75 CA CA A3394 1555 1555 2.29 LINK OE2 GLU A 80 CA CA A3394 1555 1555 2.34 LINK CA CA A3394 O HOH A3398 1555 1555 2.32 LINK CA CA A3394 O HOH A3408 1555 1555 2.32 SITE 1 AC1 6 GLU A 70 ASN A 72 VAL A 75 GLU A 80 SITE 2 AC1 6 HOH A3398 HOH A3408 SITE 1 AC2 15 ASN A 97 LEU A 99 ASP A 189 SER A 190 SITE 2 AC2 15 GLN A 192 SER A 214 TRP A 215 GLY A 216 SITE 3 AC2 15 GLY A 219 CYS A 220 GLY A 226 HOH A3488 SITE 4 AC2 15 HOH A3489 HOH A3491 HOH A3492 CRYST1 63.290 69.400 63.900 90.00 90.00 90.00 P 21 21 21 4 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 0.015800 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015649 0.00000