HEADER HYDROLASE/HYDROLASE INHIBITOR 17-JUL-97 5GDS TITLE HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE OF HUMAN TITLE 2 ALPHA-THROMBIN:HIRUNORM V COMPLEX CAVEAT 5GDS NAG H 400 HAS WRONG CHIRALITY AT ATOM C2 NAG H 400 HAS WRONG CAVEAT 2 5GDS CHIRALITY AT ATOM C4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-THROMBIN; COMPND 3 CHAIN: L; COMPND 4 EC: 3.4.21.5; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ALPHA-THROMBIN; COMPND 7 CHAIN: H; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HIRUNORM V; COMPND 11 CHAIN: I; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BLOOD; SOURCE 6 TISSUE: PLASMA; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 ORGAN: BLOOD; SOURCE 12 TISSUE: PLASMA; SOURCE 13 MOL_ID: 3 KEYWDS SERINE PROTEASE-INHIBITOR COMPLEX, THROMBIN, THROMBIN SYNTHETIC KEYWDS 2 INHIBITORS, ANTITHROMBOTICS, HIRUNORMS, HIRUDIN-LIKE BINDING MODE, KEYWDS 3 BLOOD COAGULATION, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.DE SIMONE,A.LOMBARDI,S.GALDIERO,F.NASTRI,R.DELLA MORTE,N.STAIANO, AUTHOR 2 C.PEDONE,M.BOLOGNESI,V.PAVONE REVDAT 5 09-AUG-23 5GDS 1 REMARK HETSYN REVDAT 4 29-JUL-20 5GDS 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 13-JUL-11 5GDS 1 VERSN REVDAT 2 24-FEB-09 5GDS 1 VERSN REVDAT 1 21-JAN-98 5GDS 0 JRNL AUTH G.DE SIMONE,A.LOMBARDI,S.GALDIERO,F.NASTRI,R.DELLA MORTE, JRNL AUTH 2 N.STAIANO,C.PEDONE,M.BOLOGNESI,V.PAVONE JRNL TITL HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE JRNL TITL 2 OF HUMAN ALPHA-THROMBIN-HIRUNORM V COMPLEX. JRNL REF PROTEIN SCI. V. 7 243 1998 JRNL REFN ISSN 0961-8368 JRNL PMID 9521099 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.LOMBARDI,F.NASTRI,R.DELLA MORTE,A.ROSSI,A.DE ROSA, REMARK 1 AUTH 2 N.STAIANO,C.PEDONE,V.PAVONE REMARK 1 TITL RATIONAL DESIGN OF TRUE HIRUDIN MIMETICS: SYNTHESIS AND REMARK 1 TITL 2 CHARACTERIZATION OF MULTISITE-DIRECTED ALPHA-THROMBIN REMARK 1 TITL 3 INHIBITORS REMARK 1 REF J.MED.CHEM. V. 39 2008 1996 REMARK 1 REFN ISSN 0022-2623 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.J.RYDEL,A.TULINSKY,W.BODE,R.HUBER REMARK 1 TITL REFINED STRUCTURE OF THE HIRUDIN-THROMBIN COMPLEX REMARK 1 REF J.MOL.BIOL. V. 221 583 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 21609 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1760 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21609 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2476 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 28.700 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.018 ; 18.000; 3483 REMARK 3 BOND ANGLES (DEGREES) : 2.800 ; 40.000; 3474 REMARK 3 TORSION ANGLES (DEGREES) : 17.835; 7.000 ; 1503 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.021 ; 29.000; 62 REMARK 3 GENERAL PLANES (A) : 0.021 ; 99.000; 362 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : 0.230 ; 25.000; 81 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.83 REMARK 3 BSOL : 158.7 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE REGIONS WITH INTERRUPTED ELECTRON DENSITIES ARE FOUND REMARK 3 IN THE N-TERMINAL AND C-TERMINAL REGIONS OF CHAIN L, THE REMARK 3 C-TERMINAL REGION OF CHAIN H, AND SOME RESIDUES IN THE REMARK 3 AUTOLYSIS LOOP. THESE REGIONS INCLUDE: THR L 1H - REMARK 3 GLU L 1C; ASP L 14L - ARG L 15; THR H 147 AND TRP H 148; REMARK 3 GLY H 246 AND GLU H 247. RESIDUES THR H 149 - LYS H 149E REMARK 3 IN THE GAMMA AUTOLYSIS LOOP ARE FOUND WITH NO ELECTRON REMARK 3 DENSITIES AND ARE NOT INCLUDED IN THIS ENTRY. THERE IS REMARK 3 NO ELECTRON DENSITY FOT HIRUNORM V RESIDUES I 5 - I 15. REMARK 3 OTHER ATOMS WITH NO DENSITY ARE GIVEN OCCUPANCY VALUES OF REMARK 3 0.00 IN THIS ENTRY. REMARK 4 REMARK 4 5GDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000179714. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, CCP4 REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: THE STRUCTURE WAS ANALYZED REMARK 200 BY DIFFERENCE FOURIER TECHNIQUES REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 1HAH (J. VIJAYALAKSHMI ET AL., 1994, REMARK 200 PROTEIN SCI. 3,2254-71) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTALS OF THROMBIN:HIRUNORM V REMARK 280 COMPLEX WERE GROWN, AS DESCRIBED BY SKRZYPEZAK ET AL. (1991) J. REMARK 280 MOL. BIOL.,221,1379-1393 BY VAPOR DIFFUSION METHODS AT 4 C. A 6 REMARK 280 MICROLITER DROP, CONTAINING 0.05 M SODIUM HEPES (PH 7.0) 10% (W/ REMARK 280 V) PEG 4000 0.02% NAN3, 20 MG/ML. THROMBIN:HIRUNORM V COMPLEX REMARK 280 WAS EQUILIBRATED AGAINST A PRECIPITATING SOLUTION CONTAINING 0.1 REMARK 280 M SODIUM HEPES (PH 7.0) 20% (W/V) PEG 4000 0.04% NAN3. CRYSTAL REMARK 280 OF THROMBIN:HIRUGEN COMPLEX WERE CRUSHED AND INDIVIDUAL SEEDS REMARK 280 WERE USED FOR CROSS-SEEDING EXPERIMENTS., VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 35.95000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.95000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.40000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I 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 400 REMARK 400 COMPOUND REMARK 400 THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN REMARK 400 INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN REMARK 400 INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN REMARK 400 INDICATOR *I* IS USED FOR HIRUNORM V INHIBITOR. 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 THR H 148A REMARK 465 ALA H 148B REMARK 465 ASN H 148C REMARK 465 VAL H 148D REMARK 465 GLY H 148E REMARK 465 LYS H 148F REMARK 465 ASP I 5 REMARK 465 DAL I 6 REMARK 465 GLY I 7 REMARK 465 BAL I 8 REMARK 465 PRO I 9 REMARK 465 GLU I 10 REMARK 465 SER I 11 REMARK 465 HIS I 12 REMARK 465 HMF I 13 REMARK 465 GLY I 14 REMARK 465 GLY I 15 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 THR L 1H REMARK 475 PHE L 1G REMARK 475 GLY L 1F REMARK 475 SER L 1E REMARK 475 GLY L 1D REMARK 475 ASP L 14L REMARK 475 GLY L 14M REMARK 475 ARG L 15 REMARK 475 TRP H 148 REMARK 475 GLU H 247 REMARK 475 TYR I 24 REMARK 475 ALC I 25 REMARK 475 DGL I 26 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU L 1C CB CG CD OE1 OE2 REMARK 480 GLU L 13 CD OE1 OE2 REMARK 480 LYS L 14A CG CD CE NZ REMARK 480 ARG L 14D CD NE CZ NH1 NH2 REMARK 480 GLU L 14H OE1 OE2 REMARK 480 ILE L 14K C O REMARK 480 GLU H 18 CD OE1 OE2 REMARK 480 SER H 36A CB OG REMARK 480 GLN H 38 CD OE1 NE2 REMARK 480 GLU H 39 CD OE1 OE2 REMARK 480 ARG H 50 CG CD NE CZ NH1 NH2 REMARK 480 ASN H 62 CG OD1 ND2 REMARK 480 LYS H 81 CD CE NZ REMARK 480 GLU H 86 OE1 OE2 REMARK 480 LYS H 87 CD CE NZ REMARK 480 LYS H 107 CE NZ REMARK 480 LYS H 109 CE NZ REMARK 480 LYS H 110 CG CD CE NZ REMARK 480 ARG H 126 CD NE CZ NH1 NH2 REMARK 480 GLU H 127 CG CD OE1 OE2 REMARK 480 GLN H 131 OE1 NE2 REMARK 480 LYS H 145 CE NZ REMARK 480 THR H 147 O CB OG1 CG2 REMARK 480 GLY H 150 N REMARK 480 GLN H 151 CG CD OE1 NE2 REMARK 480 LYS H 169 CD CE NZ REMARK 480 ASP H 186A CG OD1 OD2 REMARK 480 LYS H 186D CD CE NZ REMARK 480 GLU H 192 CD OE1 OE2 REMARK 480 ASN H 205 OD1 ND2 REMARK 480 ARG H 233 CZ NH1 REMARK 480 LYS H 235 NZ REMARK 480 LYS H 236 CG CD CE NZ REMARK 480 TRP H 237 N REMARK 480 GLN H 239 CG CD OE1 NE2 REMARK 480 LYS H 240 CD CE NZ REMARK 480 ASP H 243 CG OD1 OD2 REMARK 480 GLN H 244 CD OE1 NE2 REMARK 480 GLY H 246 C O REMARK 480 GLU I 19 CD OE1 OE2 REMARK 480 AIB I 22 CB1 REMARK 480 AIB I 23 O CB1 CB2 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 N GLU H 146 O HOH H 523 2.12 REMARK 500 ND2 ASN H 60G O5 NAG H 400 2.16 REMARK 500 ND2 ASN H 60G C2 NAG H 400 2.17 REMARK 500 CG ASN H 60G C1 NAG H 400 2.18 REMARK 500 O HOH H 403 O HOH H 462 2.18 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 ASP L 14L NH2 ARG H 173 4556 1.75 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 GLU L 8 CD GLU L 8 OE2 0.068 REMARK 500 GLU L 14C CD GLU L 14C OE2 0.083 REMARK 500 GLU H 23 CD GLU H 23 OE2 0.075 REMARK 500 GLU H 61 CD GLU H 61 OE2 0.099 REMARK 500 ARG H 75 CB ARG H 75 CG 0.174 REMARK 500 GLU H 80 CD GLU H 80 OE1 0.072 REMARK 500 GLU H 97A CD GLU H 97A OE2 0.090 REMARK 500 GLU H 164 CD GLU H 164 OE2 0.078 REMARK 500 GLU H 217 CD GLU H 217 OE2 0.072 REMARK 500 GLU I 18 CD GLU I 18 OE2 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 ASP L 1A CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP L 14 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP L 14 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 SER H 27 N - CA - CB ANGL. DEV. = 11.5 DEGREES REMARK 500 ASP H 49 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP H 49 CB - CG - OD2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ASP H 60E CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG H 77A NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG H 93 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG H 97 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP H 100 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP H 100 CB - CG - OD2 ANGL. DEV. = -9.0 DEGREES REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP H 102 CB - CG - OD2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ASP H 125 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP H 125 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP H 170 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP H 186A CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG H 206 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG H 206 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP H 221 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG H 221A NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP I 16 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 PRO I 21 C - N - CA ANGL. DEV. = 9.1 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 L 1E 5.63 51.99 REMARK 500 PHE L 7 -84.68 -130.23 REMARK 500 TYR L 14J 24.28 -79.04 REMARK 500 ILE L 14K 31.63 70.78 REMARK 500 ASP L 14L 104.12 93.59 REMARK 500 TYR H 60A 75.00 -159.11 REMARK 500 HIS H 71 -60.04 -133.75 REMARK 500 GLU H 77 80.79 -69.09 REMARK 500 GLU H 97A -63.77 -132.99 REMARK 500 LYS H 186D 132.00 -170.53 REMARK 500 TYR I 24 -38.59 -16.96 REMARK 500 ALC I 25 -89.08 -58.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN H 156 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 NAG H 400 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS REMARK 999 USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE REMARK 999 STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8, REMARK 999 3467-3475). DBREF 5GDS L 1 15 UNP P00734 THRB_HUMAN 328 363 DBREF 5GDS H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 5GDS I 1 26 PDB 5GDS 5GDS 1 26 SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 I 26 CHG VAL NAL THR ASP DAL GLY BAL PRO GLU SER HIS HMF SEQRES 2 I 26 GLY GLY ASP TYR GLU GLU ILE PRO AIB AIB TYR ALC DGL MODRES 5GDS ASN H 60G ASN GLYCOSYLATION SITE MODRES 5GDS NAL I 3 ALA BETA-(2-NAPHTHYL)-ALANINE MODRES 5GDS AIB I 22 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 5GDS AIB I 23 ALA ALPHA-AMINOISOBUTYRIC ACID MODRES 5GDS ALC I 25 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID HET CHG I 1 10 HET NAL I 3 15 HET AIB I 22 6 HET AIB I 23 6 HET ALC I 25 10 HET DGL I 26 10 HET NAG H 400 14 HETNAM CHG CYCLOHEXYL-GLYCINE HETNAM NAL BETA-(2-NAPHTHYL)-ALANINE HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM ALC 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID HETNAM DGL D-GLUTAMIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 3 CHG C8 H15 N O2 FORMUL 3 NAL C13 H13 N O2 FORMUL 3 AIB 2(C4 H9 N O2) FORMUL 3 ALC C9 H17 N O2 FORMUL 3 DGL C5 H9 N O4 FORMUL 4 NAG C8 H15 N O6 FORMUL 5 HOH *133(H2 O) HELIX 1 1 GLU L 8 LYS L 10 5 3 HELIX 2 2 GLU L 14C SER L 14I 1 7 HELIX 3 3 ALA H 56 CYS H 58 5 3 HELIX 4 4 PRO H 60B TRP H 60D 5 3 HELIX 5 5 GLU H 61 ASP H 63 5 3 HELIX 6 6 ARG H 126 LEU H 129C 1 7 HELIX 7 7 ARG H 165 SER H 171 1 7 HELIX 8 8 PRO H 186 GLU H 186B 5 3 HELIX 9 9 PHE H 232 PHE H 245 5 14 SHEET 1 A 4 LYS H 81 MET H 84 0 SHEET 2 A 4 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 A 4 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 A 4 GLU H 39 SER H 45 -1 N ALA H 44 O VAL H 31 SHEET 1 B 3 TRP H 51 THR H 54 0 SHEET 2 B 3 ALA H 104 LEU H 108 -1 N MET H 106 O VAL H 52 SHEET 3 B 3 LEU H 85 ILE H 90 -1 N TYR H 89 O LEU H 105 SHEET 1 C 2 LYS H 135 GLY H 140 0 SHEET 2 C 2 GLN H 156 PRO H 161 -1 N LEU H 160 O GLY H 136 SHEET 1 D 4 MET H 180 ALA H 183 0 SHEET 2 D 4 GLY H 226 HIS H 230 -1 N TYR H 228 O PHE H 181 SHEET 3 D 4 TRP H 207 TRP H 215 -1 N TRP H 215 O PHE H 227 SHEET 4 D 4 PRO H 198 LYS H 202 -1 N MET H 201 O TYR H 208 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.00 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.03 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.06 LINK ND2 ASN H 60G C1 NAG H 400 1555 1555 1.39 LINK C CHG I 1 N VAL I 2 1555 1555 1.34 LINK C VAL I 2 N NAL I 3 1555 1555 1.34 LINK C PRO I 21 N AIB I 22 1555 1555 1.35 LINK C AIB I 22 N AIB I 23 1555 1555 1.33 LINK C AIB I 23 N TYR I 24 1555 1555 1.34 LINK C TYR I 24 N ALC I 25 1555 1555 1.32 LINK C ALC I 25 N DGL I 26 1555 1555 1.33 CISPEP 1 SER H 36A PRO H 37 0 2.86 SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195 CRYST1 71.900 72.800 73.300 90.00 100.70 90.00 C 1 2 1 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 0.013908 0.000000 0.002628 0.00000 SCALE2 0.000000 0.013736 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013884 0.00000