HEADER HYDROLASE/HYDROLASE INHIBITOR 11-JUN-12 4AX9 TITLE HUMAN THROMBIN COMPLEXED WITH NAPSAGATRAN, RO0466240 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: THROMBIN HEAVY CHAIN, RESIDUES 364-620; COMPND 5 SYNONYM: THROMBIN, COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT COMPND 6 1, ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN COMPND 7 HEAVY CHAIN; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HIRUDIN VARIANT-1; COMPND 11 CHAIN: I; COMPND 12 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 55-65; COMPND 13 SYNONYM: HIRUDIN, HIRUDIN-1, HIRUDIN-I, LEPIRUDIN; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: PROTHROMBIN; COMPND 16 CHAIN: L; COMPND 17 FRAGMENT: THROMBIN LIGHT CHAIN, RESIDUES 334-361; COMPND 18 SYNONYM: THROMBIN, COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT COMPND 19 1, ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN COMPND 20 HEAVY CHAIN; COMPND 21 EC: 3.4.21.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 7 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 8 ORGANISM_TAXID: 6421; SOURCE 9 ORGAN: SALIVARY GLAND; SOURCE 10 MOL_ID: 3; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX, HYDROLASE HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.W.BANNER,A.D'ARCY,F.K.WINKLER,K.HILPERT,S.SPINELLI,C.CAMBILLAU REVDAT 6 16-OCT-24 4AX9 1 REMARK REVDAT 5 01-MAY-24 4AX9 1 HETSYN REVDAT 4 29-JUL-20 4AX9 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 16-SEP-15 4AX9 1 SOURCE REVDAT 2 07-AUG-13 4AX9 1 REMARK REVDAT 1 20-JUN-12 4AX9 0 JRNL AUTH K.HILPERT,J.ACKERMANN,D.W.BANNER,A.GAST,K.GUBERNATOR, JRNL AUTH 2 P.HADVARY,L.LABLER,K.MULLER,G.SCHMID,T.B.TSCHOPP JRNL TITL DESIGN AND SYNTHESIS OF POTENT AND HIGHLY SELECTIVE THROMBIN JRNL TITL 2 INHIBITORS. JRNL REF J.MED.CHEM. V. 37 3889 1994 JRNL REFN ISSN 0022-2623 JRNL PMID 7966150 JRNL DOI 10.1021/JM00049A008 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0025 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 25336 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 : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1353 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1135 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2341 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.19000 REMARK 3 B22 (A**2) : -0.43000 REMARK 3 B33 (A**2) : 0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.710 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2493 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3377 ; 1.490 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 6.111 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;33.065 ;23.559 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 436 ;12.907 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.272 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 349 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1907 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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 IN REFMAC, BUT NOT OUTPUT. REMARK 4 REMARK 4 4AX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290052837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-93 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25336 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 71.0 REMARK 200 DATA REDUNDANCY : 2.150 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.09 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: IN HOUSE STRUCTURES REMARK 200 REMARK 200 REMARK: SOME DATA PROCESSING INFORMATION HAS BEEN LOST. A SECOND REMARK 200 DATA COLLECTION RUN WAS MERGED TO GIVE GOOD COMPLETENESS. REMARK 200 CRYSTALS GROWN, SOAKED AND DATA COLLECTED BY S. SPINELLI AND REMARK 200 C.CAMBILLAU UNDER CONTRACT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 35.70000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.02000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.70000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.02000 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: 3590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, I, L 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CZ ARG H 75 LIES ON A SPECIAL POSITION. REMARK 375 HOH H2066 LIES ON A SPECIAL POSITION. 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 149 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 TRP H 148 CA C O CB CG CD1 CD2 REMARK 470 TRP H 148 NE1 CE2 CE3 CZ2 CZ3 CH2 REMARK 470 GLN I 11 CA C O CB CG CD OE1 REMARK 470 GLN I 11 NE2 REMARK 470 ASP L 15 CA C O CB CG OD1 OD2 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 NZ LYS L 9 O HOH L 2004 2.19 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 TYR H 60A 81.59 -151.45 REMARK 500 ASN H 60G 81.73 -156.96 REMARK 500 HIS H 71 -57.55 -132.74 REMARK 500 ILE H 79 -63.72 -122.51 REMARK 500 ASN H 98 10.12 -143.22 REMARK 500 PRO I 6 141.07 -39.39 REMARK 500 LEU I 10 -118.48 -101.82 REMARK 500 PHE L 7 -85.85 -127.66 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 NA H1244 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 79.9 REMARK 620 3 PHE H 204A O 97.1 99.7 REMARK 620 4 HOH H2141 O 66.9 77.4 164.0 REMARK 620 5 HOH H2142 O 81.6 161.3 80.2 97.6 REMARK 620 6 HOH H2145 O 170.7 91.0 86.0 109.6 107.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1245 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 93.0 REMARK 620 3 HOH H2159 O 159.4 70.3 REMARK 620 4 HOH H2160 O 87.7 92.1 81.2 REMARK 620 5 HOH H2166 O 97.0 81.4 92.4 172.1 REMARK 620 6 HOH H2180 O 106.3 159.8 89.6 82.9 101.8 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AXL RELATED DB: PDB REMARK 900 HUMAN CATHEPSIN L APO FORM WITH ZN REMARK 900 RELATED ID: 4AXM RELATED DB: PDB REMARK 900 TRIAZINE CATHEPSIN INHIBITOR COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE N-TERMINAL RESIDUE IS MODIFIED DBREF 4AX9 H 16 245 UNP P00734 THRB_HUMAN 364 620 DBREF 4AX9 I 1 11 UNP P01050 HIRV1_HIRME 55 65 DBREF 4AX9 L 1A 15 UNP P00734 THRB_HUMAN 334 361 SEQRES 1 H 257 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 257 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 257 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 257 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 257 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 257 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 257 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 257 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 257 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 257 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 257 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 257 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 257 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 257 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 257 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 257 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 257 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 257 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 257 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 257 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE SEQRES 1 I 11 ASP PHE GLU GLU ILE PRO GLU GLU TYR LEU GLN SEQRES 1 L 28 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 L 28 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 L 28 ILE ASP MODRES 4AX9 ASN H 60G ASN GLYCOSYLATION SITE HET NA H1244 1 HET NA H1245 1 HET N5N H1246 39 HET NAG H1247 14 HETNAM NA SODIUM ION HETNAM N5N 2-[[(2S)-4-[[(3S)-1-CARBAMIMIDOYLPIPERIDIN-3- HETNAM 2 N5N YL]METHYLAMINO]-2-(NAPHTHALEN-2-YLSULFONYLAMINO)-4- HETNAM 3 N5N OXIDANYLIDENE-BUTANOYL] -CYCLOPROPYL-AMINO]ETHANOIC HETNAM 4 N5N ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN N5N NAPSAGATRAN; RO-46-6240 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 4 NA 2(NA 1+) FORMUL 6 N5N C26 H34 N6 O6 S FORMUL 7 NAG C8 H15 N O6 FORMUL 8 HOH *217(H2 O) HELIX 1 1 ALA H 55 CYS H 58 5 4 HELIX 2 2 PRO H 60B ASP H 60E 5 4 HELIX 3 3 THR H 60I ASN H 62 5 3 HELIX 4 4 ASP H 125 LEU H 130 1 9 HELIX 5 5 GLU H 164 SER H 171 1 8 HELIX 6 6 LYS H 185 GLY H 186C 5 5 HELIX 7 7 LEU H 234 PHE H 245 1 12 HELIX 8 8 PRO I 6 LEU I 10 5 5 HELIX 9 9 PHE L 7 SER L 11 5 5 HELIX 10 10 THR L 14B TYR L 14J 1 9 SHEET 1 HA 7 SER H 20 ASP H 21 0 SHEET 2 HA 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 HA 7 LYS H 135 GLY H 140 -1 O GLY H 136 N LEU H 160 SHEET 4 HA 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139 SHEET 5 HA 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 HA 7 GLY H 226 HIS H 230 -1 O PHE H 227 N SER H 214 SHEET 7 HA 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228 SHEET 1 HB 7 GLN H 30 ARG H 35 0 SHEET 2 HB 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 HB 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 HB 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 HB 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 HB 7 LEU H 64 ILE H 68 -1 O LEU H 64 N LEU H 85 SHEET 7 HB 7 GLN H 30 ARG H 35 -1 O MET H 32 N ARG H 67 SHEET 1 HC 2 LEU H 60 TYR H 60A 0 SHEET 2 HC 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS H 42 CYS H 58 1555 1555 2.00 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.04 SSBOND 3 CYS H 168 CYS H 182 1555 1555 1.96 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.02 LINK ND2 ASN H 60G C1 NAG H1247 1555 1555 1.45 LINK O LYS H 169 NA NA H1244 1555 1555 2.55 LINK O THR H 172 NA NA H1244 1555 1555 2.38 LINK O PHE H 204A NA NA H1244 4546 1555 2.49 LINK O ARG H 221A NA NA H1245 1555 1555 2.36 LINK O LYS H 224 NA NA H1245 1555 1555 2.34 LINK NA NA H1244 O HOH H2141 1555 1555 2.75 LINK NA NA H1244 O HOH H2142 1555 1555 2.48 LINK NA NA H1244 O HOH H2145 1555 1555 2.23 LINK NA NA H1245 O HOH H2159 1555 1555 2.48 LINK NA NA H1245 O HOH H2160 1555 1555 2.71 LINK NA NA H1245 O HOH H2166 1555 1555 2.36 LINK NA NA H1245 O HOH H2180 1555 1555 2.38 CISPEP 1 SER H 36A PRO H 37 0 -5.78 CRYST1 71.400 72.040 72.700 90.00 100.80 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 0.014006 0.000000 0.002672 0.00000 SCALE2 0.000000 0.013881 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014003 0.00000