HEADER HYDROLASE/HYDROLASE INHIBITOR 18-OCT-11 3U98
TITLE HUMAN THROMBIN IN COMPLEX WITH MI001
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN;
COMPND 3 CHAIN: L;
COMPND 4 EC: 3.4.21.5;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: THROMBIN HEAVY CHAIN;
COMPND 7 CHAIN: H;
COMPND 8 EC: 3.4.21.5;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: HIRUDIN VARIANT-2;
COMPND 11 CHAIN: I;
COMPND 12 FRAGMENT: RESIDUES IN UNP 60-72;
COMPND 13 ENGINEERED: YES
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 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS;
SOURCE 12 ORGANISM_COMMON: MEDICINAL LEECH;
SOURCE 13 ORGANISM_TAXID: 6421;
SOURCE 14 OTHER_DETAILS: SYNTHETIC FRAGMENT OF HIRUDIN FROM HIRUDO MEDICINALIS
KEYWDS SERINE PROTEASE, KRINGLE, HYDROLASE, BLOOD COAGULATION, BLOOD
KEYWDS 2 CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, CLEAVAGE ON PAIRS OF
KEYWDS 3 BASIC RESIDUES, HIRUDIN, GLYCOSYLATION, BLOOD, HYDROLASE-HYDROLASE
KEYWDS 4 INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.BIELA,A.HEINE,G.KLEBE
REVDAT 4 06-DEC-23 3U98 1 REMARK
REVDAT 3 01-NOV-23 3U98 1 HETSYN
REVDAT 2 29-JUL-20 3U98 1 COMPND REMARK HETNAM LINK
REVDAT 2 2 1 SITE
REVDAT 1 24-OCT-12 3U98 0
JRNL AUTH A.BIELA,F.SIELAFF,A.HEINE,T.STEINMETZER,G.KLEBE
JRNL TITL THROMBIN INHIBITION
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.45 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.56
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7
REMARK 3 NUMBER OF REFLECTIONS : 56456
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.165
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.187
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060
REMARK 3 FREE R VALUE TEST SET COUNT : 2856
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 22.5650 - 3.9293 0.73 2195 122 0.1779 0.1849
REMARK 3 2 3.9293 - 3.1215 0.91 2687 147 0.1459 0.1657
REMARK 3 3 3.1215 - 2.7276 0.93 2775 153 0.1650 0.2082
REMARK 3 4 2.7276 - 2.4786 0.94 2799 133 0.1714 0.1873
REMARK 3 5 2.4786 - 2.3011 0.95 2813 147 0.1636 0.2023
REMARK 3 6 2.3011 - 2.1656 0.95 2799 146 0.1578 0.2054
REMARK 3 7 2.1656 - 2.0572 0.96 2811 169 0.1576 0.1638
REMARK 3 8 2.0572 - 1.9677 0.95 2828 150 0.1520 0.1940
REMARK 3 9 1.9677 - 1.8920 0.94 2767 153 0.1550 0.1822
REMARK 3 10 1.8920 - 1.8267 0.93 2726 163 0.1579 0.1729
REMARK 3 11 1.8267 - 1.7696 0.93 2767 132 0.1473 0.1687
REMARK 3 12 1.7696 - 1.7191 0.93 2662 163 0.1548 0.1792
REMARK 3 13 1.7191 - 1.6738 0.93 2721 160 0.1555 0.1814
REMARK 3 14 1.6738 - 1.6330 0.92 2741 126 0.1566 0.1616
REMARK 3 15 1.6330 - 1.5959 0.92 2745 127 0.1627 0.1561
REMARK 3 16 1.5959 - 1.5619 0.91 2631 153 0.1681 0.2137
REMARK 3 17 1.5619 - 1.5307 0.88 2625 140 0.1809 0.1977
REMARK 3 18 1.5307 - 1.5018 0.87 2540 131 0.2066 0.2191
REMARK 3 19 1.5018 - 1.4750 0.84 2459 120 0.2216 0.2670
REMARK 3 20 1.4750 - 1.4500 0.84 2509 121 0.2295 0.2470
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.20
REMARK 3 SHRINKAGE RADIUS : 0.95
REMARK 3 K_SOL : 0.39
REMARK 3 B_SOL : 50.05
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.820
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 12.71
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.83
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.00860
REMARK 3 B22 (A**2) : -1.58370
REMARK 3 B33 (A**2) : -0.42490
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -2.48990
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.008 2504
REMARK 3 ANGLE : 1.117 3401
REMARK 3 CHIRALITY : 0.077 353
REMARK 3 PLANARITY : 0.005 432
REMARK 3 DIHEDRAL : 17.176 977
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 10
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: (CHAIN H AND RESID 16:37)
REMARK 3 ORIGIN FOR THE GROUP (A): 7.1013 -1.5850 12.6081
REMARK 3 T TENSOR
REMARK 3 T11: 0.1220 T22: 0.1387
REMARK 3 T33: 0.1143 T12: 0.0500
REMARK 3 T13: -0.0301 T23: -0.0378
REMARK 3 L TENSOR
REMARK 3 L11: 0.1946 L22: 0.3348
REMARK 3 L33: 0.1355 L12: -0.1508
REMARK 3 L13: 0.0830 L23: 0.1011
REMARK 3 S TENSOR
REMARK 3 S11: 0.2244 S12: 0.2133 S13: -0.2072
REMARK 3 S21: -0.1988 S22: -0.1741 S23: 0.1761
REMARK 3 S31: 0.1073 S32: -0.0462 S33: 0.0208
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: (CHAIN H AND RESID 38:50)
REMARK 3 ORIGIN FOR THE GROUP (A): 15.7110 1.4956 10.3865
REMARK 3 T TENSOR
REMARK 3 T11: 0.1893 T22: 0.1769
REMARK 3 T33: 0.1102 T12: 0.0739
REMARK 3 T13: -0.0024 T23: -0.0059
REMARK 3 L TENSOR
REMARK 3 L11: 0.6451 L22: 0.1993
REMARK 3 L33: 0.2323 L12: -0.1668
REMARK 3 L13: 0.0363 L23: 0.1735
REMARK 3 S TENSOR
REMARK 3 S11: 0.2294 S12: 0.4292 S13: -0.0076
REMARK 3 S21: -0.3593 S22: -0.1537 S23: -0.0702
REMARK 3 S31: 0.2251 S32: 0.1410 S33: -0.0233
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: (CHAIN H AND RESID 51:122)
REMARK 3 ORIGIN FOR THE GROUP (A): 18.6439 -0.3986 11.6836
REMARK 3 T TENSOR
REMARK 3 T11: 0.1095 T22: 0.1758
REMARK 3 T33: 0.0882 T12: 0.0702
REMARK 3 T13: 0.0117 T23: 0.0058
REMARK 3 L TENSOR
REMARK 3 L11: 0.5208 L22: 0.6375
REMARK 3 L33: 0.6283 L12: 0.0155
REMARK 3 L13: 0.0001 L23: 0.1926
REMARK 3 S TENSOR
REMARK 3 S11: 0.1524 S12: 0.2451 S13: -0.0008
REMARK 3 S21: -0.1401 S22: -0.1231 S23: -0.1136
REMARK 3 S31: 0.0492 S32: 0.1260 S33: 0.0010
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: (CHAIN H AND RESID 123:136)
REMARK 3 ORIGIN FOR THE GROUP (A): 11.8129 6.8786 33.9204
REMARK 3 T TENSOR
REMARK 3 T11: 0.1638 T22: 0.1538
REMARK 3 T33: 0.1099 T12: 0.0415
REMARK 3 T13: -0.0262 T23: -0.0378
REMARK 3 L TENSOR
REMARK 3 L11: 0.6641 L22: 0.5567
REMARK 3 L33: 0.1771 L12: 0.1993
REMARK 3 L13: 0.2259 L23: 0.2151
REMARK 3 S TENSOR
REMARK 3 S11: -0.1157 S12: -0.3128 S13: 0.1821
REMARK 3 S21: 0.2764 S22: 0.1209 S23: 0.0304
REMARK 3 S31: 0.0572 S32: 0.0886 S33: 0.0160
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: (CHAIN H AND RESID 137:199)
REMARK 3 ORIGIN FOR THE GROUP (A): 8.9620 -8.2916 26.7366
REMARK 3 T TENSOR
REMARK 3 T11: 0.1258 T22: 0.0853
REMARK 3 T33: 0.1240 T12: 0.0072
REMARK 3 T13: -0.0051 T23: -0.0011
REMARK 3 L TENSOR
REMARK 3 L11: 0.5922 L22: 0.7313
REMARK 3 L33: 0.3780 L12: -0.5921
REMARK 3 L13: 0.1430 L23: -0.4133
REMARK 3 S TENSOR
REMARK 3 S11: 0.0169 S12: -0.0187 S13: -0.2138
REMARK 3 S21: 0.0761 S22: 0.0321 S23: 0.1181
REMARK 3 S31: 0.0953 S32: -0.0131 S33: -0.0364
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: (CHAIN H AND RESID 200:246)
REMARK 3 ORIGIN FOR THE GROUP (A): 15.3525 1.7054 26.0157
REMARK 3 T TENSOR
REMARK 3 T11: 0.0770 T22: 0.0651
REMARK 3 T33: 0.0840 T12: 0.0105
REMARK 3 T13: 0.0096 T23: -0.0056
REMARK 3 L TENSOR
REMARK 3 L11: 0.8055 L22: 0.7054
REMARK 3 L33: 0.6895 L12: -0.7192
REMARK 3 L13: 0.1112 L23: -0.0008
REMARK 3 S TENSOR
REMARK 3 S11: 0.0329 S12: -0.0608 S13: 0.0239
REMARK 3 S21: 0.0390 S22: 0.0010 S23: -0.0346
REMARK 3 S31: 0.0121 S32: 0.0445 S33: -0.0153
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: (CHAIN I AND RESID 55:65)
REMARK 3 ORIGIN FOR THE GROUP (A): 11.9095 -1.6947 -3.0115
REMARK 3 T TENSOR
REMARK 3 T11: 0.4259 T22: 0.5604
REMARK 3 T33: -0.0021 T12: 0.2486
REMARK 3 T13: 0.0988 T23: -0.1165
REMARK 3 L TENSOR
REMARK 3 L11: 0.0024 L22: 0.0440
REMARK 3 L33: 0.0086 L12: -0.0061
REMARK 3 L13: -0.0033 L23: 0.0124
REMARK 3 S TENSOR
REMARK 3 S11: 0.0858 S12: 0.1927 S13: -0.0080
REMARK 3 S21: -0.1648 S22: 0.0073 S23: -0.0082
REMARK 3 S31: -0.0460 S32: -0.0594 S33: 0.1398
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: (CHAIN L AND RESID 1C:3)
REMARK 3 ORIGIN FOR THE GROUP (A): 9.7853 16.9004 19.7339
REMARK 3 T TENSOR
REMARK 3 T11: 0.1687 T22: 0.1288
REMARK 3 T33: 0.1884 T12: -0.0041
REMARK 3 T13: -0.0337 T23: 0.0108
REMARK 3 L TENSOR
REMARK 3 L11: 0.6953 L22: 0.1222
REMARK 3 L33: 0.3254 L12: -0.1289
REMARK 3 L13: 0.1985 L23: -0.1969
REMARK 3 S TENSOR
REMARK 3 S11: -0.0116 S12: 0.0220 S13: 0.1768
REMARK 3 S21: 0.0715 S22: 0.0184 S23: -0.1362
REMARK 3 S31: -0.1897 S32: 0.1416 S33: 0.0183
REMARK 3 TLS GROUP : 9
REMARK 3 SELECTION: (CHAIN L AND RESID 4:12)
REMARK 3 ORIGIN FOR THE GROUP (A): -0.9738 14.6161 17.5896
REMARK 3 T TENSOR
REMARK 3 T11: 0.0623 T22: 0.0646
REMARK 3 T33: 0.1009 T12: 0.1543
REMARK 3 T13: 0.0449 T23: -0.0327
REMARK 3 L TENSOR
REMARK 3 L11: 0.1444 L22: 0.0420
REMARK 3 L33: 0.0733 L12: -0.0210
REMARK 3 L13: 0.0475 L23: -0.0207
REMARK 3 S TENSOR
REMARK 3 S11: -0.0271 S12: -0.0563 S13: 0.0458
REMARK 3 S21: -0.1006 S22: -0.1054 S23: 0.0264
REMARK 3 S31: -0.0707 S32: -0.0605 S33: -0.1243
REMARK 3 TLS GROUP : 10
REMARK 3 SELECTION: (CHAIN L AND RESID 13:14K)
REMARK 3 ORIGIN FOR THE GROUP (A): -2.2270 5.9180 29.9045
REMARK 3 T TENSOR
REMARK 3 T11: 0.1241 T22: 0.1591
REMARK 3 T33: 0.1484 T12: 0.0338
REMARK 3 T13: 0.0330 T23: 0.0064
REMARK 3 L TENSOR
REMARK 3 L11: 0.3753 L22: 0.7870
REMARK 3 L33: 1.0741 L12: -0.0794
REMARK 3 L13: -0.5977 L23: -0.0206
REMARK 3 S TENSOR
REMARK 3 S11: 0.0242 S12: -0.1693 S13: -0.0720
REMARK 3 S21: 0.1121 S22: 0.0927 S23: 0.2982
REMARK 3 S31: 0.0337 S32: -0.3138 S33: -0.0159
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3U98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-11.
REMARK 100 THE DEPOSITION ID IS D_1000068465.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-NOV-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : BESSY
REMARK 200 BEAMLINE : 14.2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : COLLIMATING MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59463
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2
REMARK 200 DATA REDUNDANCY : 3.000
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05900
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9
REMARK 200 DATA REDUNDANCY IN SHELL : 2.90
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.45300
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 1H8D
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG8000, 20MM SODIUM PHOSPHATE,
REMARK 280 175MM SODIUM CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277.15K
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 35.15000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.75000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.15000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.75000
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: 4090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12560 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 HOH H1078 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 L 1H
REMARK 465 PHE L 1G
REMARK 465 GLY L 1F
REMARK 465 SER L 1E
REMARK 465 GLY L 1D
REMARK 465 ASP L 14L
REMARK 465 GLY L 14M
REMARK 465 ARG L 15
REMARK 465 TRP H 148
REMARK 465 THR H 149
REMARK 465 ALA H 149A
REMARK 465 ASN H 149B
REMARK 465 VAL H 149C
REMARK 465 GLY H 149D
REMARK 465 LYS H 149E
REMARK 465 GLU H 247
REMARK 465 ASN I 53
REMARK 465 GLY I 54
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 GLU L 1C CG CD OE1 OE2
REMARK 470 LYS L 14A CG CD CE NZ
REMARK 470 SER H 36A OG
REMARK 470 LYS H 110 CG CD CE NZ
REMARK 470 ASP H 186A CG OD1 OD2
REMARK 470 GLN H 239 CG CD OE1 NE2
REMARK 470 LYS H 240 CG CD CE NZ
REMARK 470 GLU I 58 CG CD OE1 OE2
REMARK 470 GLU I 61 CG CD OE1 OE2
REMARK 470 GLN I 65 CG CD OE1 NE2
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 L 7 -88.17 -128.07
REMARK 500 TYR H 60A 82.23 -153.19
REMARK 500 ASN H 60G 83.29 -157.16
REMARK 500 HIS H 71 -60.52 -128.67
REMARK 500 ILE H 79 -61.10 -126.68
REMARK 500 ASN H 95 79.68 -100.53
REMARK 500 ASN H 98 10.80 -142.00
REMARK 500 SER H 195 131.54 -35.56
REMARK 500
REMARK 500 REMARK: NULL
REMARK 630
REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE THROMBIN INHIBITOR
REMARK 630 MOLECULE NAME: (2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO-
REMARK 630 PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL)METHYL]PYRROLIDINE-2-
REMARK 630 CARBOXAMIDE
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 BJA H 1
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: PMS DAR PRO 00S
REMARK 630 DETAILS: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3RLW RELATED DB: PDB
REMARK 900 RELATED ID: 3RLY RELATED DB: PDB
REMARK 900 RELATED ID: 3RM0 RELATED DB: PDB
REMARK 900 RELATED ID: 3RM2 RELATED DB: PDB
REMARK 900 RELATED ID: 3RML RELATED DB: PDB
REMARK 900 RELATED ID: 3RMM RELATED DB: PDB
REMARK 900 RELATED ID: 3U9A RELATED DB: PDB
DBREF 3U98 L 1H 15 UNP P00734 THRB_HUMAN 328 363
DBREF 3U98 H 16 247 UNP P00734 THRB_HUMAN 364 622
DBREF 3U98 I 53 65 UNP P09945 HIRV2_HIRME 60 72
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 13 ASN GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN
MODRES 3U98 ASN H 60G ASN GLYCOSYLATION SITE
MODRES 3U98 TYS I 63 TYR O-SULFO-L-TYROSINE
HET TYS I 63 16
HET NAG H 260G 14
HET BJA H 1 39
HET PO4 H 2 5
HET NA H 3 1
HET NA H 4 1
HETNAM TYS O-SULFO-L-TYROSINE
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM BJA (2S)-1-[(2R)-2-(BENZYLSULFONYLAMINO)-5-GUANIDINO-
HETNAM 2 BJA PENTANOYL]-N-[(4-CARBAMIMIDOYLPHENYL)
HETNAM 3 BJA METHYL]PYRROLIDINE-2-CARBOXAMIDE
HETNAM PO4 PHOSPHATE ION
HETNAM NA SODIUM ION
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 TYS C9 H11 N O6 S
FORMUL 4 NAG C8 H15 N O6
FORMUL 5 BJA C26 H36 N8 O4 S
FORMUL 6 PO4 O4 P 3-
FORMUL 7 NA 2(NA 1+)
FORMUL 9 HOH *344(H2 O)
HELIX 1 1 PHE L 7 SER L 11 5 5
HELIX 2 2 THR L 14B TYR L 14J 1 9
HELIX 3 3 ALA H 55 CYS H 58 5 4
HELIX 4 4 PRO H 60B ASP H 60E 5 4
HELIX 5 5 THR H 60I ASN H 62 5 3
HELIX 6 6 ASP H 125 LEU H 130 1 9
HELIX 7 7 GLU H 164 SER H 171 1 8
HELIX 8 8 LYS H 185 GLY H 186C 5 5
HELIX 9 9 LEU H 234 GLY H 246 1 13
HELIX 10 10 PRO I 60 LEU I 64 5 5
SHEET 1 A 7 SER H 20 ASP H 21 0
SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20
SHEET 3 A 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158
SHEET 4 A 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137
SHEET 5 A 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201
SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215
SHEET 7 A 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228
SHEET 1 B 7 GLN H 30 ARG H 35 0
SHEET 2 B 7 GLU H 39 LEU H 46 -1 O LEU H 41 N LEU H 33
SHEET 3 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45
SHEET 4 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54
SHEET 5 B 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107
SHEET 6 B 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81
SHEET 7 B 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65
SHEET 1 C 2 LEU H 60 TYR H 60A 0
SHEET 2 C 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.06
SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.04
SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03
SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04
LINK ND2 ASN H 60G C1 NAG H 260G 1555 1555 1.43
LINK C GLU I 62 N TYS I 63 1555 1555 1.33
LINK C TYS I 63 N LEU I 64 1555 1555 1.33
CISPEP 1 SER H 36A PRO H 37 0 -2.58
CRYST1 70.300 71.500 72.200 90.00 100.40 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 0.014225 0.000000 0.002611 0.00000
SCALE2 0.000000 0.013986 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014082 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
