HEADER HYDROLASE 24-AUG-99 1QL9 TITLE FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRYPSINOGEN, BETA-TRYPSIN; COMPND 5 EC: 3.4.21.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: VARIANT X99RT\: RAT TRYPSIN CONTAINING THE "99"-LOOP COMPND 9 OF FACTOR XA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: PANCREAS; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: YEAST; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PYT KEYWDS SERINE PROTEASE, HYDROLASE, SERINE PROTEINASE EXPDTA X-RAY DIFFRACTION AUTHOR M.T.STUBBS REVDAT 5 05-JUL-17 1QL9 1 REMARK REVDAT 4 02-JUN-09 1QL9 1 HEADER SEQADV JRNL REVDAT 3 24-FEB-09 1QL9 1 VERSN REVDAT 2 17-MAR-05 1QL9 1 JRNL REVDAT 1 25-AUG-00 1QL9 0 JRNL AUTH S.REYDA,C.SOHN,G.KLEBE,K.RALL,D.ULLMANN,H.D.JAKUBKE, JRNL AUTH 2 M.T.STUBBS JRNL TITL RECONSTRUCTING THE BINDING SITE OF FACTOR XA IN TRYPSIN JRNL TITL 2 REVEALS LIGAND-INDUCED STRUCTURAL PLASTICITY JRNL REF J.MOL.BIOL. V. 325 963 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12527302 JRNL DOI 10.1016/S0022-2836(02)01337-2 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.RENATUS,W.BODE,R.HUBER,J.STUERZEBECHER,M.T.STUBBS REMARK 1 TITL STRUCTURAL AND FUNCTIONAL ANALYSES OF BENZAMIDINE-BASED REMARK 1 TITL 2 INHIBITORS IN COMPLEX WITH TRYPSIN: IMPLICATIONS FOR THE REMARK 1 TITL 3 INHIBITION OF FACTOR XA, TPA, AND UROKINASE REMARK 1 REF J.MED.CHEM. V. 41 5445 1998 REMARK 1 REFN ISSN 0022-2623 REMARK 1 PMID 9876114 REMARK 1 DOI 10.1021/JM981068G REMARK 1 REFERENCE 2 REMARK 1 AUTH M.T.STUBBS REMARK 1 TITL STRUCTURAL ASPECTS OF FACTOR XA INHIBITION REMARK 1 REF CURR.PHARM.DES. V. 2 543 1996 REMARK 1 REFN ISSN 1381-6128 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.T.STUBBS,R.HUBER,W.BODE REMARK 1 TITL CRYSTAL STRUCTURES OF FACTOR XA SPECIFIC INHIBITORS IN REMARK 1 TITL 2 COMPLEX WITH TRYPSIN: STRUCTURAL GROUNDS FOR INHIBITION OF REMARK 1 TITL 3 FACTOR XA AND SELECTIVITY AGAINST THROMBIN REMARK 1 REF FEBS LETT. V. 375 103 1995 REMARK 1 REFN ISSN 0014-5793 REMARK 1 PMID 7498454 REMARK 1 DOI 10.1016/0014-5793(95)01190-P REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14100 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 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 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 714 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1670 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.690 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.210 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QL9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1290002920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-98 REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : 7.00 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16310 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45600 REMARK 200 R SYM FOR SHELL (I) : 0.45600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25MM TRIS PH7, 10MM CACL2, 40% MGSO4, REMARK 280 PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 62.07000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 62.07000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 62.07000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 62.07000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 62.07000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 62.07000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 62.07000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 62.07000 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 62.07000 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 62.07000 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 62.07000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 62.07000 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 62.07000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 62.07000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 62.07000 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 62.07000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 62.07000 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 62.07000 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 62.07000 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 62.07000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 62.07000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 62.07000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 62.07000 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 62.07000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 62.07000 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 62.07000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 THE 223 AMINO ACIDS OF RAT TRYPSIN ARE IDENTIFIED BY THE REMARK 400 RESIDUE NUMBERS OF THE HOMOLOGOUS CHYMOTRYPSINOGEN. REMARK 400 REMARK 400 THE BINDING MODE OF THE INHIBITOR IS NOT AS EXPECTED: THE REMARK 400 CHLORINATED NAPHTHALENE MOIETY REACHES DEEP INTO THE REMARK 400 PRIMARY SPECIFICITY POCKET, WHERE THE BURIED WATER MOLECULE REMARK 400 W416 IS DISPLACED BY THE CHLORINE ATOM REMARK 400 (COMPARE WITH DAIICHI STRUCTURE 1MTW.PDB). CONCOMMITANT REMARK 400 WITH THIS, (I) THE HYDROXYL FUNCTION OF SER190 (ALA IN FXA) REMARK 400 ROTATES AWAY FROM THE INHIBITOR (II) A NEW WATER MOLECULE REMARK 400 (PROVOCATIVELY LABELLED W416) APPEARS, COORDINATED BY REMARK 400 ASP189OD2, GLY219O, ASN224O, AND W329 (W415) (III) THE REMARK 400 PEPTIDE BOND SER217-GLY219 FLIPS REMARK 400 (MAYBE TO ALLOW CLOSER APPROACH OF GLY219O TO W216) (IV) REMARK 400 THE SIDE CHAIN OF TYR217 FLIPS UP TO FORM ONE SIDE OF A REMARK 400 NOVEL "HYDROPHOBIC BOX", MIMICKING THE FACTOR XA STRUCTURE REMARK 400 (ALTHOUGH WITH A DIFFERENT APPROACH TO PHE174) THE REMARK 400 PIPERIDINYLPYRIDINE MOITIES OCCUPY LOCATIONS STRONGLY REMARK 400 REMINISCENT OF THE DX9065A:TRYPSIN COMPLEXES REMARK 400 (CF 1MTS.PDB, 1MTU.PDB, 1MTV.PDB); THE WEAKLY BASIC REMARK 400 PYRIDINE WOULD OCCUPY THE "CATION HOLE" OF FACTOR XA REMARK 400 REMARK 400 THE SAME INHIBITOR HAS ALSO BEEN CRYSTALLIZED (A) WITH REMARK 400 BOVINE TRYPSIN AT PH 8 (SEE PDB FILE EBI-2917), WHICH SHOWS REMARK 400 SIMILAR STRUCTURAL REARRANGEMENTS, AND (B) WITH BOVINE REMARK 400 TRYPSIN AT PH7, WHERE IT BINDS IN THE REVERSE DIRECTION REMARK 400 (SEE PDB FILE EBI-2919) 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 HIS A 71 -66.06 -135.67 REMARK 500 ASN A 115 -159.29 -152.95 REMARK 500 SER A 214 -70.03 -117.05 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 A 480 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE1 REMARK 620 2 ASN A 72 O 85.2 REMARK 620 3 VAL A 75 O 170.4 86.5 REMARK 620 4 GLU A 77 OE1 99.1 77.1 83.7 REMARK 620 5 GLU A 80 OE2 97.7 158.0 91.9 80.9 REMARK 620 6 HOH A2016 O 81.9 105.9 95.8 176.9 96.1 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 480 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZEN A 999 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QL7 RELATED DB: PDB REMARK 900 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN REMARK 900 RELATED ID: 1QL8 RELATED DB: PDB REMARK 900 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN REMARK 900 RELATED ID: 1MTW RELATED DB: PDB REMARK 900 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN REMARK 900 RELATED ID: 1MTS RELATED DB: PDB REMARK 900 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN REMARK 900 RELATED ID: 1MTU RELATED DB: PDB REMARK 900 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN REMARK 900 RELATED ID: 1MTV RELATED DB: PDB REMARK 900 FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH BOVINE TRYPSIN SEE REMARK 900 ALSO THE PDB ENTRIES: 1ANB 1ANC 1AND 1ANE 1AMH 1SLU 1SLV 1SLW 1SLX REMARK 900 1DPO 3TGI 3TGJ DBREF 1QL9 A 16 245 UNP P00763 TRY2_RAT 24 246 SEQADV 1QL9 GLU A 97 UNP P00763 LYS 102 ENGINEERED MUTATION SEQADV 1QL9 TYR A 99 UNP P00763 LEU 104 ENGINEERED MUTATION SEQRES 1 A 223 ILE VAL GLY GLY TYR THR CYS GLN GLU ASN SER 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 ASP GLN TRP VAL VAL SER ALA ALA SEQRES 4 A 223 HIS CYS TYR LYS SER ARG ILE GLN VAL ARG LEU GLY GLU SEQRES 5 A 223 HIS ASN ILE ASN VAL LEU GLU GLY ASN GLU GLN PHE VAL SEQRES 6 A 223 ASN ALA ALA LYS ILE ILE LYS HIS PRO ASN PHE ASP ARG SEQRES 7 A 223 GLU THR TYR ASN ASN ASP ILE MET LEU ILE LYS LEU SER SEQRES 8 A 223 SER PRO VAL LYS LEU ASN ALA ARG VAL ALA THR VAL ALA SEQRES 9 A 223 LEU PRO SER SER CYS ALA PRO ALA GLY THR GLN CYS LEU SEQRES 10 A 223 ILE SER GLY TRP GLY ASN THR LEU SER SER GLY VAL ASN SEQRES 11 A 223 GLU PRO ASP LEU LEU GLN CYS LEU ASP ALA PRO LEU LEU SEQRES 12 A 223 PRO GLN ALA ASP CYS GLU ALA SER TYR PRO GLY LYS ILE SEQRES 13 A 223 THR ASP ASN MET VAL CYS VAL GLY PHE 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 ASN GLY GLU LEU GLN GLY ILE VAL SER TRP GLY TYR SEQRES 16 A 223 GLY CYS ALA LEU PRO ASP ASN PRO GLY VAL TYR THR LYS SEQRES 17 A 223 VAL CYS ASN TYR VAL ASP TRP ILE GLN ASP THR ILE ALA SEQRES 18 A 223 ALA ASN HET CA A 480 1 HET SO4 A 600 5 HET ZEN A 999 34 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM ZEN [4-(6-CHLORO-NAPHTHALENE-2-SULFONYL)-PIPERAZIN-1-YL]- HETNAM 2 ZEN (3,4,5,6-TETRAHYDRO-2H-[1,4']BIPYRIDINYL-4-YL)- HETNAM 3 ZEN METHANONE FORMUL 2 CA CA 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 ZEN C25 H27 CL N4 O3 S FORMUL 5 HOH *70(H2 O) HELIX 1 1 ALA A 55 TYR A 59 5 5 HELIX 2 2 PRO A 164 TYR A 172 1 9 HELIX 3 3 TYR A 234 ALA A 244 1 11 SHEET 1 A 7 GLN A 81 ASN A 84 0 SHEET 2 A 7 GLN A 64 LEU A 68 -1 N LEU A 68 O GLN A 81 SHEET 3 A 7 GLN A 30 ASN A 34 -1 N ASN A 34 O GLN A 64 SHEET 4 A 7 HIS A 40 ASN A 48 -1 N GLY A 44 O VAL A 31 SHEET 5 A 7 TRP A 51 SER A 54 -1 N VAL A 53 O SER A 45 SHEET 6 A 7 MET A 104 LEU A 108 -1 N ILE A 106 O VAL A 52 SHEET 7 A 7 ALA A 85 LYS A 90 -1 N ILE A 89 O LEU A 105 SHEET 1 B 2 GLN A 135 GLY A 140 0 SHEET 2 B 2 GLN A 156 PRO A 161 -1 N ALA A 160 O CYS A 136 SHEET 1 C 4 MET A 180 VAL A 183 0 SHEET 2 C 4 GLY A 226 LYS A 230 -1 N TYR A 228 O VAL A 181 SHEET 3 C 4 GLU A 204 TRP A 215 -1 N TRP A 215 O VAL A 227 SHEET 4 C 4 PRO A 198 CYS A 201 -1 N CYS A 201 O GLU A 204 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 2.03 SSBOND 4 CYS A 136 CYS A 201 1555 1555 2.03 SSBOND 5 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 6 CYS A 191 CYS A 220 1555 1555 2.03 LINK CA CA A 480 OE1 GLU A 70 1555 1555 2.34 LINK CA CA A 480 O ASN A 72 1555 1555 2.26 LINK CA CA A 480 O VAL A 75 1555 1555 2.22 LINK CA CA A 480 OE1 GLU A 77 1555 1555 3.07 LINK CA CA A 480 OE2 GLU A 80 1555 1555 2.41 LINK CA CA A 480 O HOH A2016 1555 1555 2.21 SITE 1 AC1 6 GLU A 70 ASN A 72 VAL A 75 GLU A 77 SITE 2 AC1 6 GLU A 80 HOH A2016 SITE 1 AC2 5 HIS A 57 GLN A 192 GLY A 193 SER A 195 SITE 2 AC2 5 ZEN A 999 SITE 1 AC3 20 THR A 98 TYR A 99 LEU A 145 GLY A 148 SITE 2 AC3 20 VAL A 149 LYS A 175 SER A 190 GLN A 192 SITE 3 AC3 20 SER A 195 VAL A 213 TRP A 215 GLY A 216 SITE 4 AC3 20 TYR A 217 GLY A 219 CYS A 220 GLY A 226 SITE 5 AC3 20 VAL A 227 TYR A 228 SO4 A 600 HOH A2070 CRYST1 124.140 124.140 124.140 90.00 90.00 90.00 I 2 3 24 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 0.008055 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008055 0.00000