HEADER HYDROLASE/HYDROLASE INHIBITOR 21-MAR-99 8KME TITLE CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2770. COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN; COMPND 3 CHAIN: 1; COMPND 4 FRAGMENT: LIGHT CHAIN; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN; COMPND 8 CHAIN: 2; COMPND 9 FRAGMENT: HEAVY CHAIN; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: N-ACETYLHIRUDIN; COMPND 13 CHAIN: 3; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: SYNTHETIC; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: SEL2770; COMPND 18 CHAIN: 4; COMPND 19 ENGINEERED: YES; COMPND 20 OTHER_DETAILS: SYNTHETIC 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: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 4; SOURCE 12 SYNTHETIC: YES KEYWDS THROMBIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, SELECTIDE EXPDTA X-RAY DIFFRACTION AUTHOR I.MOCHALKIN,A.TULINSKY REVDAT 6 15-NOV-23 8KME 1 REMARK REVDAT 5 20-SEP-23 8KME 1 LINK REVDAT 4 04-OCT-17 8KME 1 REMARK REVDAT 3 13-JUL-11 8KME 1 VERSN REVDAT 2 24-FEB-09 8KME 1 VERSN REVDAT 1 24-MAR-99 8KME 0 JRNL AUTH I.MOCHALKIN,A.TULINSKY JRNL TITL STRUCTURES OF THROMBIN RETRO-INHIBITED WITH SEL2711 AND JRNL TITL 2 SEL2770 AS THEY RELATE TO FACTOR XA BINDING. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 785 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10089309 JRNL DOI 10.1107/S0907444999000359 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 60.0 REMARK 3 NUMBER OF REFLECTIONS : 19578 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.167 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 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2352 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 103 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) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.015 ; 0.014 REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 0.036 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.050 ; 0.046 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.040 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.150 ; 0.170 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.600 ; 0.240 REMARK 3 MULTIPLE TORSION (A) : 0.600 ; 0.280 REMARK 3 H-BOND (X...Y) (A) : 0.600 ; 0.280 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.000 ; 0.900 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.500 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; 2.100 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.000 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8KME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-97 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.3 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 RU200 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 : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS (RIGAKU) REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13507 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 (%) : 60.0 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.04900 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 37.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1HAH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM PHASPATE BUFFER, PH 7.3 REMARK 280 28 % PEG 8000 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 35.83000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.83000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.00000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2, 3, 4 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 REMARK 400 THE N~2~-{(2S)-2-[(N-ACETYL-4-CARBAMIMIDOYL-L-PHENYLALANYL)AMINO]-2- REMARK 400 CYCLOHEXYLACETYL}-N~6~,N~6~-DIMETHYL-L-LYSYL- L-LEUCYL-L- REMARK 400 PROLINAMIDE IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: N~2~-{(2S)-2-[(N-ACETYL-4-CARBAMIMIDOYL-L-PHENYLALANYL) REMARK 400 AMINO]-2-CYCLOHEXYLACETYL}-N~6~,N~6~-DIMETHYL-L-LYSYL- L- REMARK 400 LEUCYL-L-PROLINAMIDE REMARK 400 CHAIN: 4 REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 1 1H REMARK 465 PHE 1 1G REMARK 465 GLY 1 1F REMARK 465 SER 1 1E REMARK 465 GLY 1 1D REMARK 465 GLU 1 1C REMARK 465 ILE 1 14K REMARK 465 ASP 1 14L REMARK 465 GLY 1 14M REMARK 465 ARG 1 14N REMARK 465 TRP 2 147A REMARK 465 THR 2 147B REMARK 465 ALA 2 147C REMARK 465 ASN 2 147D REMARK 465 VAL 2 147E REMARK 465 GLY 2 147F REMARK 465 LYS 2 147G REMARK 465 GLY 2 246 REMARK 465 GLU 2 247 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 ARG 2 35 CG CD NE CZ NH1 NH2 REMARK 470 ARG 2 75 CG CD NE CZ NH1 NH2 REMARK 470 ASP 2 243 CG OD1 OD2 REMARK 470 GLN 2 244 CB CG CD OE1 NE2 REMARK 470 GLU 3 358 CB CG CD OE1 OE2 REMARK 470 GLU 3 361 CB CG CD OE1 OE2 REMARK 470 GLU 3 362 CB CG CD OE1 OE2 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 CHG 4 385 C MLY 4 389 N 0.151 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 ARG 1 4 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG 2 73 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG 2 73 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG 2 73 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG 2 77A NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG 2 101 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP 2 125 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG 2 126 CD - NE - CZ ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG 2 126 NE - CZ - NH1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG 2 126 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG 2 175 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET 2 180 O - C - N ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG 2 187 CG - CD - NE ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG 2 187 CD - NE - CZ ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG 2 187 NE - CZ - NH1 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG 2 187 NE - CZ - NH2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP 2 194 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP 2 194 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG 2 206 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG 2 221A CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG 2 221A NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG 2 233 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG 2 233 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 LEU 4 390 C - N - CA ANGL. DEV. = 15.0 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 PHE 1 7 -87.84 -130.96 REMARK 500 PRO 2 37 179.26 -59.57 REMARK 500 GLN 2 38 73.79 -102.10 REMARK 500 ALA 2 44 -173.72 176.18 REMARK 500 TYR 2 60A 82.42 -162.78 REMARK 500 ASN 2 60G 85.97 -166.85 REMARK 500 HIS 2 71 -47.05 -140.91 REMARK 500 ARG 2 77A -49.89 -23.52 REMARK 500 GLU 2 86 -8.56 -141.58 REMARK 500 LYS 2 87 111.21 169.44 REMARK 500 GLU 2 97A -75.45 -105.26 REMARK 500 ARG 2 101 47.01 80.22 REMARK 500 ASN 2 143 158.79 -45.96 REMARK 500 ASN 2 179 20.42 -73.73 REMARK 500 PRO 2 186 -15.71 -45.01 REMARK 500 ASP 2 189 155.94 174.08 REMARK 500 SER 2 195 155.57 -42.17 REMARK 500 GLN 2 244 -18.98 -47.85 REMARK 500 LEU 4 390 104.88 43.89 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 MLY 4 389 LEU 4 390 -94.13 REMARK 500 LEU 4 390 PRO 4 391 144.00 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 ARG 2 93 0.15 SIDE CHAIN REMARK 500 ARG 2 165 0.21 SIDE CHAIN REMARK 500 ARG 2 187 0.16 SIDE CHAIN REMARK 500 ARG 2 206 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU 1 3 10.31 REMARK 500 VAL 2 66 17.01 REMARK 500 ILE 2 88 11.51 REMARK 500 ASP 2 100 17.56 REMARK 500 MET 2 106 10.64 REMARK 500 ALA 2 129 -12.24 REMARK 500 VAL 2 158 13.46 REMARK 500 LEU 2 160 -15.02 REMARK 500 PHE 2 199 12.75 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 2 950 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS 2 169 O REMARK 620 2 THR 2 172 O 74.6 REMARK 620 3 HOH 2 463 O 74.6 77.9 REMARK 620 4 HOH 2 465 O 173.6 99.9 107.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA 2 951 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG 2 221A O REMARK 620 2 LYS 2 224 O 81.9 REMARK 620 3 HOH 2 440 O 91.3 111.6 REMARK 620 4 HOH 2 462 O 96.4 138.5 109.8 REMARK 620 5 HOH 2 570 O 159.4 80.7 105.4 89.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA 2 950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA 2 951 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN 3 OF N-ACETYLHIRUDIN REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN 4 OF SEL2770 REMARK 800 REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *1* REMARK 999 IS USED FOR RESIDUES 1H - 15 AND CHAIN INDICATOR *2* IS USED FOR REMARK 999 RESIDUES 16 - 247. CHAIN INDICATOR *3* IS USED FOR N-ACETYLHIRUDIN REMARK 999 355 - 364 WITH SULFATO-TYR AT 363. DBREF 8KME 1 1B 14J UNP P00734 THRB_HUMAN 328 363 DBREF 8KME 2 16 245 UNP P00734 THRB_HUMAN 364 622 DBREF 8KME 3 355 364 PDB 8KME 8KME 355 364 DBREF 8KME 4 379 392 PDB 8KME 8KME 379 392 SEQRES 1 1 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 1 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 1 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 2 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 2 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 2 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 2 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 2 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 2 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 2 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 2 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 2 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 2 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 2 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 2 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 2 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 2 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 2 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 2 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 2 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 2 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 2 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 2 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 3 10 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU SEQRES 1 4 7 ACE 0BN CHG MLY LEU PRO NH2 MODRES 8KME TYS 3 363 TYR O-SULFO-L-TYROSINE MODRES 8KME 0BN 4 380 PHE 4-CARBAMIMIDOYL-L-PHENYLALANINE MODRES 8KME MLY 4 389 LYS N-DIMETHYL-LYSINE HET TYS 3 363 16 HET ACE 4 379 3 HET 0BN 4 380 14 HET CHG 4 385 10 HET MLY 4 389 11 HET NH2 4 392 1 HET NA 2 950 1 HET NA 2 951 1 HETNAM TYS O-SULFO-L-TYROSINE HETNAM ACE ACETYL GROUP HETNAM 0BN 4-CARBAMIMIDOYL-L-PHENYLALANINE HETNAM CHG CYCLOHEXYL-GLYCINE HETNAM MLY N-DIMETHYL-LYSINE HETNAM NH2 AMINO GROUP HETNAM NA SODIUM ION FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 ACE C2 H4 O FORMUL 4 0BN C10 H13 N3 O2 FORMUL 4 CHG C8 H15 N O2 FORMUL 4 MLY C8 H18 N2 O2 FORMUL 4 NH2 H2 N FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *103(H2 O) HELIX 1 1 GLU 1 8 LYS 1 10 5 3 HELIX 2 2 GLU 1 14C GLU 1 14H 1 6 HELIX 3 3 ALA 2 56 CYS 2 58 5 3 HELIX 4 4 PRO 2 60B TRP 2 60D 5 3 HELIX 5 5 GLU 2 61 ASP 2 63 5 3 HELIX 6 6 ARG 2 126 LEU 2 129C 1 7 HELIX 7 7 ARG 2 165 SER 2 171 1 7 HELIX 8 8 PHE 2 232 ASP 2 243 5 12 SHEET 1 A 4 LYS 2 81 MET 2 84 0 SHEET 2 A 4 LEU 2 64 ILE 2 68 -1 N ILE 2 68 O LYS 2 81 SHEET 3 A 4 GLN 2 30 ARG 2 35 -1 N PHE 2 34 O LEU 2 65 SHEET 4 A 4 LEU 2 40 SER 2 45 -1 N ALA 2 44 O VAL 2 31 SHEET 1 B 2 TRP 2 51 THR 2 54 0 SHEET 2 B 2 ALA 2 104 LYS 2 107 -1 N MET 2 106 O VAL 2 52 SHEET 1 C 2 LYS 2 135 GLY 2 140 0 SHEET 2 C 2 GLN 2 156 PRO 2 161 -1 N LEU 2 160 O GLY 2 136 SHEET 1 D 4 MET 2 180 ALA 2 183 0 SHEET 2 D 4 GLY 2 226 HIS 2 230 -1 N TYR 2 228 O PHE 2 181 SHEET 3 D 4 TRP 2 207 TRP 2 215 -1 N TRP 2 215 O PHE 2 227 SHEET 4 D 4 PRO 2 198 LYS 2 202 -1 N MET 2 201 O TYR 2 208 SSBOND 1 CYS 1 1 CYS 2 122 1555 1555 2.04 SSBOND 2 CYS 2 42 CYS 2 58 1555 1555 2.14 SSBOND 3 CYS 2 168 CYS 2 182 1555 1555 2.09 SSBOND 4 CYS 2 191 CYS 2 220 1555 1555 2.06 LINK C GLU 3 362 N TYS 3 363 1555 1555 1.35 LINK C TYS 3 363 N LEU 3 364 1555 1555 1.33 LINK C ACE 4 379 N 0BN 4 380 1555 1555 1.27 LINK C 0BN 4 380 N CHG 4 385 1555 1555 1.30 LINK C CHG 4 385 N MLY 4 389 1555 1555 1.49 LINK C MLY 4 389 N LEU 4 390 1555 1555 1.33 LINK C PRO 4 391 N NH2 4 392 1555 1555 1.37 LINK O LYS 2 169 NA NA 2 950 1555 1555 2.44 LINK O THR 2 172 NA NA 2 950 1555 1555 2.41 LINK O ARG 2 221A NA NA 2 951 1555 1555 2.54 LINK O LYS 2 224 NA NA 2 951 1555 1555 2.32 LINK O HOH 2 440 NA NA 2 951 1555 1555 2.56 LINK O HOH 2 462 NA NA 2 951 1555 1555 2.54 LINK O HOH 2 463 NA NA 2 950 1555 1555 2.99 LINK O HOH 2 465 NA NA 2 950 1555 1555 2.41 LINK O HOH 2 570 NA NA 2 951 1555 1555 2.44 CISPEP 1 SER 2 36A PRO 2 37 0 -3.85 SITE 1 AC1 4 LYS 2 169 THR 2 172 HOH 2 463 HOH 2 465 SITE 1 AC2 4 LYS 2 224 HOH 2 440 HOH 2 462 HOH 2 570 SITE 1 AC3 13 PHE 2 34 LYS 2 36 GLN 2 38 LEU 2 65 SITE 2 AC3 13 ARG 2 73 THR 2 74 TYR 2 76 GLU 2 80 SITE 3 AC3 13 LYS 2 81 ILE 2 82 HOH 3 427 HOH 3 450 SITE 4 AC3 13 HOH 3 467 SITE 1 AC4 14 LEU 2 99 ILE 2 174 ASP 2 189 ALA 2 190 SITE 2 AC4 14 GLU 2 192 SER 2 214 TRP 2 215 GLY 2 216 SITE 3 AC4 14 GLU 2 217 GLY 2 219 CYS 2 220 HOH 2 709 SITE 4 AC4 14 HOH 4 428 HOH 4 679 SITE 1 CAT 3 HIS 2 57 ASP 2 102 SER 2 195 CRYST1 71.660 72.000 73.450 90.00 101.20 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 0.013955 0.000000 0.002763 0.00000 SCALE2 0.000000 0.013889 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013879 0.00000