HEADER HYDROLASE/HYDROLASE INHIBITOR 17-OCT-11 3U8T TITLE HUMAN THROMBIN COMPLEXED WITH D-PHE-PRO-D-ARG-CYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: PROTHROMBIN; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 SYNONYM: PROTHROMBIN; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: D-PHE-PRO-D-ARG-CYS DIRECT THROMBIN INHIBITOR; COMPND 13 CHAIN: I; COMPND 14 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 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.C.FIGUEIREDO,C.C.CLEMENT,M.PHILIPP,P.J.B.PEREIRA REVDAT 4 30-OCT-24 3U8T 1 HETSYN REVDAT 3 29-JUL-20 3U8T 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 05-JUN-13 3U8T 1 REMARK REVDAT 1 11-APR-12 3U8T 0 JRNL AUTH A.C.FIGUEIREDO,C.C.CLEMENT,S.ZAKIA,J.GINGOLD,M.PHILIPP, JRNL AUTH 2 P.J.PEREIRA JRNL TITL RATIONAL DESIGN AND CHARACTERIZATION OF JRNL TITL 2 D-PHE-PRO-D-ARG-DERIVED DIRECT THROMBIN INHIBITORS. JRNL REF PLOS ONE V. 7 34354 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22457833 JRNL DOI 10.1371/JOURNAL.PONE.0034354 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28671 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1420 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 35.0010 - 4.0077 0.99 2853 169 0.1590 0.1815 REMARK 3 2 4.0077 - 3.1817 1.00 2785 132 0.1439 0.1880 REMARK 3 3 3.1817 - 2.7797 1.00 2746 133 0.1681 0.2110 REMARK 3 4 2.7797 - 2.5256 1.00 2737 129 0.1604 0.2235 REMARK 3 5 2.5256 - 2.3446 1.00 2706 138 0.1521 0.1853 REMARK 3 6 2.3446 - 2.2064 1.00 2714 139 0.1433 0.1797 REMARK 3 7 2.2064 - 2.0959 1.00 2708 126 0.1409 0.1834 REMARK 3 8 2.0959 - 2.0047 1.00 2667 154 0.1390 0.1979 REMARK 3 9 2.0047 - 1.9275 1.00 2637 153 0.1492 0.2051 REMARK 3 10 1.9275 - 1.8610 1.00 2698 147 0.1703 0.2365 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 36.15 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.810 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) : 1.47280 REMARK 3 B22 (A**2) : 0.78880 REMARK 3 B33 (A**2) : -2.26150 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.018 2412 REMARK 3 ANGLE : 1.742 3268 REMARK 3 CHIRALITY : 0.137 344 REMARK 3 PLANARITY : 0.009 414 REMARK 3 DIHEDRAL : 15.002 941 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN H AND RESID 321:406) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9859 -4.2359 -23.9412 REMARK 3 T TENSOR REMARK 3 T11: 0.0947 T22: 0.0820 REMARK 3 T33: 0.0398 T12: -0.0088 REMARK 3 T13: -0.0360 T23: 0.0394 REMARK 3 L TENSOR REMARK 3 L11: 1.1527 L22: 1.2244 REMARK 3 L33: 1.1902 L12: 0.0073 REMARK 3 L13: -0.3263 L23: -0.3266 REMARK 3 S TENSOR REMARK 3 S11: 0.0896 S12: 0.3851 S13: 0.0072 REMARK 3 S21: -0.4390 S22: -0.0169 S23: -0.0150 REMARK 3 S31: 0.0733 S32: -0.4764 S33: -0.0137 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN H AND RESID 407:565) REMARK 3 ORIGIN FOR THE GROUP (A): 15.4009 -12.9934 -10.6623 REMARK 3 T TENSOR REMARK 3 T11: 0.0485 T22: 0.0475 REMARK 3 T33: 0.0387 T12: -0.0147 REMARK 3 T13: -0.0240 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.0320 L22: 1.3493 REMARK 3 L33: 1.2841 L12: -0.0212 REMARK 3 L13: -0.0933 L23: -0.2450 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: -0.0149 S13: -0.1409 REMARK 3 S21: -0.0067 S22: 0.0344 S23: -0.0740 REMARK 3 S31: 0.1900 S32: -0.1061 S33: -0.0191 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN H AND RESID 566:577) REMARK 3 ORIGIN FOR THE GROUP (A): 30.8759 -1.4843 -14.1633 REMARK 3 T TENSOR REMARK 3 T11: 0.0563 T22: 0.1630 REMARK 3 T33: 0.3188 T12: -0.0305 REMARK 3 T13: -0.0072 T23: -0.0635 REMARK 3 L TENSOR REMARK 3 L11: 2.7156 L22: 3.0740 REMARK 3 L33: 4.7164 L12: 0.1136 REMARK 3 L13: 1.0332 L23: -1.3740 REMARK 3 S TENSOR REMARK 3 S11: 0.0557 S12: 0.1756 S13: 0.4195 REMARK 3 S21: 0.0745 S22: -0.0625 S23: -0.4200 REMARK 3 S31: -0.3592 S32: 0.7138 S33: 0.1333 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN L AND RESID 291:317) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6342 -0.6735 -1.7428 REMARK 3 T TENSOR REMARK 3 T11: 0.0890 T22: 0.1217 REMARK 3 T33: 0.0640 T12: 0.0192 REMARK 3 T13: 0.0358 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 2.2117 L22: 2.6531 REMARK 3 L33: 1.9137 L12: -0.2270 REMARK 3 L13: 0.1858 L23: -0.9279 REMARK 3 S TENSOR REMARK 3 S11: 0.0297 S12: -0.0921 S13: 0.1838 REMARK 3 S21: 0.3455 S22: 0.0864 S23: 0.3352 REMARK 3 S31: -0.1563 S32: -0.3811 S33: -0.0534 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN I AND RESID 1:4) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5976 -20.5571 -20.8418 REMARK 3 T TENSOR REMARK 3 T11: 0.3235 T22: 0.4266 REMARK 3 T33: 0.4175 T12: 0.0170 REMARK 3 T13: -0.0040 T23: -0.0566 REMARK 3 L TENSOR REMARK 3 L11: 4.9358 L22: 4.0983 REMARK 3 L33: 2.2287 L12: -4.3538 REMARK 3 L13: -2.6932 L23: 1.9346 REMARK 3 S TENSOR REMARK 3 S11: 0.2854 S12: 0.7152 S13: 0.1897 REMARK 3 S21: -0.5185 S22: -0.0061 S23: 0.1516 REMARK 3 S31: 0.0501 S32: -0.2284 S33: -0.2031 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 3U8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28722 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.861 REMARK 200 RESOLUTION RANGE LOW (A) : 34.995 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.18100 REMARK 200 R SYM FOR SHELL (I) : 0.18100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS, 50MM BICINE, 30MM NAF, 30MM REMARK 280 NABR, 30MM NAI, 11.5% MPD, 11.5% PEG-1000, 11.5% PEG-3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.71500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.71500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.55000 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE D-PHENYLALANYL-L-PROLYL-N~5~-[AMINO(IMINIO)METHYL]-D-ORNITHYL-L- REMARK 400 CYSTEINAMIDE IS PEPTIDE-LIKE, A MEMBER OF THROMBIN INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: D-PHENYLALANYL-L-PROLYL-N~5~-[AMINO(IMINIO)METHYL]-D- REMARK 400 ORNITHYL-L-CYSTEINAMIDE REMARK 400 CHAIN: I 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 H 467 REMARK 465 TRP H 468 REMARK 465 THR H 469 REMARK 465 ALA H 470 REMARK 465 ASN H 471 REMARK 465 VAL H 472 REMARK 465 GLY H 473 REMARK 465 LYS H 474 REMARK 465 GLY H 578 REMARK 465 GLU H 579 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 O HOH H 894 O HOH H 904 2.14 REMARK 500 NE2 GLN H 335 O HOH H 915 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 DAR I 3 NE DAR I 3 CZ 0.098 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 CYS I 4 CA - CB - SG ANGL. DEV. = 7.4 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 L 299 -89.71 -128.14 REMARK 500 GLU H 345 149.50 -170.64 REMARK 500 TYR H 367 80.53 -155.83 REMARK 500 ASN H 373 76.14 -160.66 REMARK 500 HIS H 386 -55.96 -123.94 REMARK 500 ASN H 394 -1.15 69.48 REMARK 500 ILE H 395 -51.85 -122.25 REMARK 500 ASN H 415 14.04 -143.47 REMARK 500 DAR I 3 -52.79 -34.92 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 H 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 553 O REMARK 620 2 LYS H 556 O 89.6 REMARK 620 3 HOH H 706 O 157.0 71.4 REMARK 620 4 HOH H 714 O 100.0 80.7 89.7 REMARK 620 5 HOH H 722 O 86.8 91.6 81.1 169.6 REMARK 620 6 HOH H 738 O 103.2 166.8 95.5 99.9 86.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3U69 RELATED DB: PDB REMARK 900 RELATED ID: 3U8O RELATED DB: PDB REMARK 900 RELATED ID: 3U8R RELATED DB: PDB DBREF 3U8T L 291 317 UNP P00734 THRB_HUMAN 334 360 DBREF 3U8T H 321 577 UNP P00734 THRB_HUMAN 364 622 DBREF 3U8T I 1 5 PDB 3U8T 3U8T 1 5 SEQRES 1 L 27 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 L 27 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 L 27 ILE 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 5 DPN PRO DAR CYS NH2 MODRES 3U8T ASN H 373 ASN GLYCOSYLATION SITE HET DPN I 1 11 HET DAR I 3 11 HET NH2 I 5 1 HET NAG H 601 14 HET NA H 602 1 HET IOD H 603 1 HET CL H 604 1 HET MPD H 605 8 HETNAM DPN D-PHENYLALANINE HETNAM DAR D-ARGININE HETNAM NH2 AMINO GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETNAM IOD IODIDE ION HETNAM CL CHLORIDE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL 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 DPN C9 H11 N O2 FORMUL 3 DAR C6 H15 N4 O2 1+ FORMUL 3 NH2 H2 N FORMUL 4 NAG C8 H15 N O6 FORMUL 5 NA NA 1+ FORMUL 6 IOD I 1- FORMUL 7 CL CL 1- FORMUL 8 MPD C6 H14 O2 FORMUL 9 HOH *265(H2 O) HELIX 1 1 PHE L 299 SER L 303 5 5 HELIX 2 2 THR L 308 TYR L 316 1 9 HELIX 3 3 ALA H 361 CYS H 364 5 4 HELIX 4 4 PRO H 368 ASP H 371 5 4 HELIX 5 5 THR H 375 ASN H 377 5 3 HELIX 6 6 ASP H 442 LEU H 450 1 9 HELIX 7 7 GLU H 489 SER H 496 1 8 HELIX 8 8 LYS H 511 GLY H 515 5 5 HELIX 9 9 LEU H 566 PHE H 577 1 12 SHEET 1 A 7 SER H 325 ASP H 326 0 SHEET 2 A 7 GLN H 481 PRO H 486 -1 O VAL H 482 N SER H 325 SHEET 3 A 7 LYS H 455 GLY H 460 -1 N VAL H 458 O VAL H 483 SHEET 4 A 7 PRO H 528 LYS H 532 -1 O VAL H 530 N ARG H 457 SHEET 5 A 7 TRP H 539 TRP H 547 -1 O TYR H 540 N MET H 531 SHEET 6 A 7 GLY H 558 HIS H 562 -1 O PHE H 559 N TRP H 547 SHEET 7 A 7 MET H 505 ALA H 508 -1 N PHE H 506 O TYR H 560 SHEET 1 B 7 LYS H 397 SER H 399 0 SHEET 2 B 7 LEU H 379 ILE H 383 -1 N ILE H 383 O LYS H 397 SHEET 3 B 7 GLN H 335 ARG H 340 -1 N PHE H 339 O LEU H 380 SHEET 4 B 7 GLU H 345 LEU H 352 -1 O GLU H 345 N ARG H 340 SHEET 5 B 7 TRP H 357 THR H 360 -1 O LEU H 359 N SER H 351 SHEET 6 B 7 ALA H 421 LEU H 425 -1 O MET H 423 N VAL H 358 SHEET 7 B 7 LEU H 401 ILE H 406 -1 N GLU H 402 O LYS H 424 SHEET 1 C 2 LEU H 366 TYR H 367 0 SHEET 2 C 2 LYS H 372 ASN H 373 -1 O LYS H 372 N TYR H 367 SSBOND 1 CYS L 293 CYS H 439 1555 1555 2.06 SSBOND 2 CYS H 348 CYS H 364 1555 1555 2.08 SSBOND 3 CYS H 493 CYS H 507 1555 1555 2.03 SSBOND 4 CYS H 521 CYS H 551 1555 1555 2.06 LINK ND2 ASN H 373 C1 NAG H 601 1555 1555 1.45 LINK C DPN I 1 N PRO I 2 1555 1555 1.35 LINK C PRO I 2 N DAR I 3 1555 1555 1.34 LINK C DAR I 3 N CYS I 4 1555 1555 1.34 LINK C CYS I 4 N NH2 I 5 1555 1555 1.45 LINK O ARG H 553 NA NA H 602 1555 1555 2.41 LINK O LYS H 556 NA NA H 602 1555 1555 2.48 LINK NA NA H 602 O HOH H 706 1555 1555 2.43 LINK NA NA H 602 O HOH H 714 1555 1555 2.39 LINK NA NA H 602 O HOH H 722 1555 1555 2.66 LINK NA NA H 602 O HOH H 738 1555 1555 2.29 CISPEP 1 SER H 342 PRO H 343 0 -5.88 CRYST1 51.800 77.100 83.430 90.00 90.00 90.00 P 21 21 21 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 0.019305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011986 0.00000