HEADER BLOOD COAGULATION 18-FEB-97 1ADX TITLE FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN (TMEGF5), NMR, 14 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBOMODULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIFTH EGF-LIKE DOMAIN; COMPND 5 SYNONYM: TMEGF5; COMPND 6 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 KEYWDS BLOOD COAGULATION, ANTICOAGULANT, FIBRINOGEN, PEPTIDE SYNTHESIS, KEYWDS 2 PROTEIN C, THROMBIN, DISULFIDE BONDS EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR B.A.SAMPOLI-BENITEZ,M.J.HUNTER,D.P.MEININGER,E.A.KOMIVES REVDAT 4 30-OCT-24 1ADX 1 REMARK REVDAT 3 16-FEB-22 1ADX 1 REMARK REVDAT 2 24-FEB-09 1ADX 1 VERSN REVDAT 1 24-DEC-97 1ADX 0 JRNL AUTH B.A.SAMPOLI BENITEZ,M.J.HUNTER,D.P.MEININGER,E.A.KOMIVES JRNL TITL STRUCTURE OF THE FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN: AN JRNL TITL 2 EGF-LIKE DOMAIN WITH A NOVEL DISULFIDE-BONDING PATTERN. JRNL REF J.MOL.BIOL. V. 273 913 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9367781 JRNL DOI 10.1006/JMBI.1997.1356 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL REFERENCE ABOVE. REMARK 4 REMARK 4 1ADX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170698. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TOCSY; NOESY DQF-COSY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX500; DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DGII, X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC 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 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 2 PRO A 10 C - N - CD ANGL. DEV. = -26.5 DEGREES REMARK 500 2 PRO A 24 C - N - CD ANGL. DEV. = -21.2 DEGREES REMARK 500 3 PRO A 24 C - N - CD ANGL. DEV. = -19.2 DEGREES REMARK 500 4 PRO A 24 C - N - CD ANGL. DEV. = -23.4 DEGREES REMARK 500 5 PRO A 10 C - N - CD ANGL. DEV. = -22.1 DEGREES REMARK 500 6 PRO A 24 C - N - CD ANGL. DEV. = -19.2 DEGREES REMARK 500 8 PRO A 10 C - N - CD ANGL. DEV. = -26.1 DEGREES REMARK 500 8 PRO A 24 C - N - CD ANGL. DEV. = -21.0 DEGREES REMARK 500 10 PRO A 24 C - N - CD ANGL. DEV. = -19.8 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 1 PHE A 3 29.48 178.85 REMARK 500 1 CYS A 4 -159.80 41.43 REMARK 500 1 GLN A 6 41.44 86.08 REMARK 500 1 THR A 7 -40.11 82.21 REMARK 500 1 ALA A 8 130.87 -174.64 REMARK 500 1 PRO A 10 -159.89 -66.28 REMARK 500 1 ASP A 12 90.41 -60.34 REMARK 500 1 CYS A 13 90.12 -59.20 REMARK 500 1 GLN A 18 96.88 -41.82 REMARK 500 1 ALA A 19 29.59 -175.14 REMARK 500 1 CYS A 23 149.46 51.69 REMARK 500 1 PRO A 24 -164.64 -53.26 REMARK 500 1 GLU A 25 90.03 -54.22 REMARK 500 1 ILE A 28 117.39 79.85 REMARK 500 1 LEU A 29 -165.42 -53.99 REMARK 500 1 PHE A 33 26.20 44.88 REMARK 500 1 ILE A 38 -38.32 -134.84 REMARK 500 1 ASP A 39 -89.52 -167.26 REMARK 500 2 MET A 2 121.11 61.55 REMARK 500 2 CYS A 4 163.50 68.42 REMARK 500 2 GLN A 6 110.34 86.41 REMARK 500 2 THR A 7 -88.90 31.42 REMARK 500 2 CYS A 9 -122.51 -157.97 REMARK 500 2 ALA A 11 100.70 66.57 REMARK 500 2 THR A 17 53.49 178.65 REMARK 500 2 GLN A 18 -164.40 -62.47 REMARK 500 2 CYS A 23 104.43 14.69 REMARK 500 2 PRO A 24 135.01 23.24 REMARK 500 2 GLU A 25 92.76 -56.62 REMARK 500 2 ILE A 28 113.30 98.45 REMARK 500 2 LEU A 29 -154.45 -60.97 REMARK 500 2 ASP A 30 173.86 101.50 REMARK 500 2 PHE A 33 19.09 54.96 REMARK 500 2 THR A 36 176.95 160.49 REMARK 500 2 ASP A 37 40.61 171.03 REMARK 500 2 ILE A 38 29.37 -159.92 REMARK 500 2 ASP A 39 67.08 171.91 REMARK 500 3 PHE A 3 53.71 -106.46 REMARK 500 3 CYS A 4 158.89 63.77 REMARK 500 3 GLN A 6 -163.95 -109.76 REMARK 500 3 CYS A 9 166.54 175.07 REMARK 500 3 PRO A 10 -160.61 -53.79 REMARK 500 3 CYS A 13 94.32 -43.07 REMARK 500 3 THR A 17 87.32 168.94 REMARK 500 3 CYS A 23 118.76 -1.25 REMARK 500 3 PRO A 24 64.77 4.08 REMARK 500 3 GLU A 25 96.14 24.05 REMARK 500 3 ILE A 28 153.40 51.75 REMARK 500 3 PHE A 33 26.66 44.89 REMARK 500 3 ASP A 37 90.87 160.83 REMARK 500 REMARK 500 THIS ENTRY HAS 277 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ADX RELATED DB: PDB DBREF 1ADX A 1 40 UNP P07204 TRBM_HUMAN 405 444 SEQRES 1 A 40 GLN MET PHE CYS ASN GLN THR ALA CYS PRO ALA ASP CYS SEQRES 2 A 40 ASP PRO ASN THR GLN ALA SER CYS GLU CYS PRO GLU GLY SEQRES 3 A 40 TYR ILE LEU ASP ASP GLY PHE ILE CYS THR ASP ILE ASP SEQRES 4 A 40 GLU SSBOND 1 CYS A 4 CYS A 9 1555 1555 2.02 SSBOND 2 CYS A 13 CYS A 21 1555 1555 2.02 SSBOND 3 CYS A 23 CYS A 35 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1