HEADER HYDROLASE/HYDROLASE INHIBITOR/RNA 04-JUN-08 3DD2 TITLE CRYSTAL STRUCTURE OF AN RNA APTAMER BOUND TO HUMAN THROMBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 6 CHAIN: H; COMPND 7 EC: 3.4.21.5; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: RNA (26-MER); COMPND 10 CHAIN: B; COMPND 11 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 THROMBIN, APTAMER, RNA, DNA, HEPARIN, EXOSITE, PROTEASE, SERINE KEYWDS 2 PROTEASE, HYDROLASE-HYDROLASE INHIBITOR-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.B.LONG,B.A.SULLENGER REVDAT 7 20-NOV-24 3DD2 1 REMARK REVDAT 6 30-AUG-23 3DD2 1 REMARK LINK REVDAT 5 25-OCT-17 3DD2 1 REMARK REVDAT 4 13-JUL-11 3DD2 1 VERSN REVDAT 3 10-FEB-09 3DD2 1 SEQRES VERSN REVDAT 2 16-DEC-08 3DD2 1 JRNL REVDAT 1 11-NOV-08 3DD2 0 JRNL AUTH S.B.LONG,M.B.LONG,R.R.WHITE,B.A.SULLENGER JRNL TITL CRYSTAL STRUCTURE OF AN RNA APTAMER BOUND TO THROMBIN. JRNL REF RNA V. 14 2504 2008 JRNL REFN ISSN 1355-8382 JRNL PMID 18971322 JRNL DOI 10.1261/RNA.1239308 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1922052.125 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 35581 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 SET) : 0.204 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1764 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4006 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 180 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2328 REMARK 3 NUCLEIC ACID ATOMS : 537 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.01000 REMARK 3 B22 (A**2) : 23.88000 REMARK 3 B33 (A**2) : -10.87000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.150 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.020 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 55.42 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA-MULTI-ENDO.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : PPACK_PATCHES.PAR REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-MULTI-ENDO.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : PPACK_PATCHES.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-02 REMARK 200 TEMPERATURE (KELVIN) : 98 REMARK 200 PH : 6.5 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37211 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35400 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1PPB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 41.88300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 67.00850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.88300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 67.00850 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 APPLY THE FOLLOWING TO CHAINS: L, H, B 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 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 DT B 26 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT B 26 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT B 26 C7 C6 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 ALA L 1B -143.43 44.35 REMARK 500 PHE L 7 -89.50 -137.20 REMARK 500 TYR H 60A 84.03 -154.70 REMARK 500 ASN H 60G 85.97 -161.25 REMARK 500 HIS H 71 -61.53 -121.71 REMARK 500 GLU H 77 78.02 -106.34 REMARK 500 ILE H 79 -65.73 -123.73 REMARK 500 SER H 214 -58.66 -122.06 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 A B 7 0.06 SIDE CHAIN REMARK 500 A B 9 0.06 SIDE CHAIN REMARK 500 G B 13 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE REMARK 600 RESIDUES: REMARK 600 1) VIA A HEMIKETAL GROUP TO OG SER H 195, REMARK 600 2) VIA A METHYLENE GROUP TO NE2 HIS H 57. 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 MG H1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221 O REMARK 620 2 LYS H 224 O 93.2 REMARK 620 3 HOH H1012 O 104.0 161.8 REMARK 620 4 HOH H1037 O 96.5 80.1 103.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 8 OP2 REMARK 620 2 A B 9 OP2 85.6 REMARK 620 3 HOH B1003 O 94.6 172.4 REMARK 620 4 HOH B1006 O 176.0 91.0 89.0 REMARK 620 5 HOH B1009 O 95.8 86.1 86.3 86.0 REMARK 620 6 HOH B1018 O 94.3 93.0 94.5 83.8 169.7 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE 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 0G6 H 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG L 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0G6 H 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG H1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P6G H1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY H1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY H1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY H1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY H1007 DBREF 3DD2 L 1D 14L UNP P00734 THRB_HUMAN 332 361 DBREF 3DD2 H 16 246 UNP P00734 THRB_HUMAN 364 621 DBREF 3DD2 B 1 26 PDB 3DD2 3DD2 1 26 SEQRES 1 L 30 GLY GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS SEQRES 2 L 30 LYS SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SEQRES 3 L 30 SER TYR ILE ASP SEQRES 1 H 258 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 258 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 258 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 258 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 258 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 258 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 258 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 258 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 258 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 258 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 258 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 258 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 258 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 258 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 258 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 258 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 258 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 258 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 258 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 258 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY SEQRES 1 B 26 G G G A A CFL A A A G CFL UFT G SEQRES 2 B 26 A A G UFT A CFL UFT UFT A CFL CFL CFL DT MODRES 3DD2 CFL B 6 DC MODRES 3DD2 CFL B 11 DC MODRES 3DD2 UFT B 12 DU MODRES 3DD2 UFT B 17 DU MODRES 3DD2 CFL B 19 DC MODRES 3DD2 UFT B 20 DU MODRES 3DD2 UFT B 21 DU MODRES 3DD2 CFL B 23 DC MODRES 3DD2 CFL B 24 DC MODRES 3DD2 CFL B 25 DC HET CFL B 6 20 HET CFL B 11 20 HET UFT B 12 20 HET UFT B 17 20 HET CFL B 19 20 HET UFT B 20 20 HET UFT B 21 20 HET CFL B 23 20 HET CFL B 24 20 HET CFL B 25 20 HET PEG L 305 7 HET 0G6 H 1 30 HET MG H1002 1 HET P6G H1003 19 HET ACY H1004 4 HET ACY H1005 4 HET ACY H1006 4 HET ACY H1007 4 HET MG B1000 1 HET ACY B 151 4 HET ACY B 152 4 HET PEG B 103 7 HET PEG B 104 7 HETNAM CFL 4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D- HETNAM 2 CFL ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE HETNAM UFT 2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETNAM MG MAGNESIUM ION HETNAM P6G HEXAETHYLENE GLYCOL HETNAM ACY ACETIC ACID HETSYN CFL 2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETSYN 0G6 PPACK HETSYN P6G POLYETHYLENE GLYCOL PEG400 FORMUL 3 CFL 6(C9 H13 F N3 O7 P) FORMUL 3 UFT 4(C9 H12 F N2 O8 P) FORMUL 4 PEG 3(C4 H10 O3) FORMUL 5 0G6 C21 H34 CL N6 O3 1+ FORMUL 6 MG 2(MG 2+) FORMUL 7 P6G C12 H26 O7 FORMUL 8 ACY 6(C2 H4 O2) FORMUL 17 HOH *253(H2 O) HELIX 1 1 PHE L 7 SER L 11 5 5 HELIX 2 2 THR L 14B ASP L 14L 1 11 HELIX 3 3 ALA H 55 LEU H 59 1 5 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 THR H 149 GLY H 149D 5 5 HELIX 8 8 GLU H 164 SER H 171 1 8 HELIX 9 9 LYS H 185 GLY H 186C 5 5 HELIX 10 10 LEU H 234 GLY H 246 1 13 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 GLY H 136 O LEU H 160 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 GLU H 39 N ARG H 35 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 MET H 106 N VAL H 52 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 2.03 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.05 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK C3 0G6 H 1 NE2 HIS H 57 1555 1555 1.49 LINK C2 0G6 H 1 OG SER H 195 1555 1555 1.43 LINK O3' A B 5 P CFL B 6 1555 1555 1.61 LINK O3' CFL B 6 P A B 7 1555 1555 1.62 LINK O3' G B 10 P CFL B 11 1555 1555 1.60 LINK O3' CFL B 11 P UFT B 12 1555 1555 1.61 LINK O3' UFT B 12 P G B 13 1555 1555 1.60 LINK O3' G B 16 P UFT B 17 1555 1555 1.61 LINK O3' UFT B 17 P A B 18 1555 1555 1.62 LINK O3' A B 18 P CFL B 19 1555 1555 1.61 LINK O3' CFL B 19 P UFT B 20 1555 1555 1.61 LINK O3' UFT B 20 P UFT B 21 1555 1555 1.61 LINK O3' UFT B 21 P A B 22 1555 1555 1.60 LINK O3' A B 22 P CFL B 23 1555 1555 1.61 LINK O3' CFL B 23 P CFL B 24 1555 1555 1.61 LINK O3' CFL B 24 P CFL B 25 1555 1555 1.61 LINK O3' CFL B 25 P DT B 26 1555 1555 1.62 LINK O ARG H 221 MG MG H1002 1555 1555 2.40 LINK O LYS H 224 MG MG H1002 1555 1555 2.45 LINK MG MG H1002 O HOH H1012 1555 1555 2.26 LINK MG MG H1002 O HOH H1037 1555 1555 2.30 LINK OP2 A B 8 MG MG B1000 1555 1555 2.06 LINK OP2 A B 9 MG MG B1000 1555 1555 2.05 LINK MG MG B1000 O HOH B1003 1555 1555 2.01 LINK MG MG B1000 O HOH B1006 1555 1555 2.30 LINK MG MG B1000 O HOH B1009 1555 1555 2.12 LINK MG MG B1000 O HOH B1018 1555 1555 2.27 CISPEP 1 SER H 36A PRO H 37 0 -0.23 SITE 1 AC1 7 A B 14 GLN H 131 ALA H 132 TYR H 134 SITE 2 AC1 7 ILE L 14K ASP L 14L HOH L 209 SITE 1 AC2 7 A B 7 A B 8 A B 9 HOH B1003 SITE 2 AC2 7 HOH B1006 HOH B1009 HOH B1018 SITE 1 AC3 17 HIS H 57 TYR H 60A LEU H 99 ASP H 189 SITE 2 AC3 17 ALA H 190 GLY H 193 SER H 195 SER H 214 SITE 3 AC3 17 TRP H 215 GLY H 216 GLY H 219 GLY H 226 SITE 4 AC3 17 HOH H 247 HOH H 248 HOH H 249 HOH H 250 SITE 5 AC3 17 HOH H1024 SITE 1 AC4 3 A B 4 A B 5 CFL B 23 SITE 1 AC5 3 G B 2 G B 3 HOH B1017 SITE 1 AC6 3 G B 3 CFL B 23 CFL B 24 SITE 1 AC7 6 CFL B 11 CFL B 19 UFT B 20 HOH B1021 SITE 2 AC7 6 HOH B1044 ALA H 149A SITE 1 AC8 6 ARG H 221 LYS H 224 HOH H1012 HOH H1032 SITE 2 AC8 6 HOH H1037 HOH H1047 SITE 1 AC9 11 GLN H 38 LEU H 65 TYR H 76 ILE H 82 SITE 2 AC9 11 SER H 129B LEU H 129C PRO H 204 PHE H 204A SITE 3 AC9 11 HOH H1127 HOH H1135 HOH H1137 SITE 1 BC1 2 ASN H 60G ACY H1007 SITE 1 BC2 2 GLY H 19 HOH H1153 SITE 1 BC3 7 PHE H 114 PRO H 120 ARG H 173 HOH H1062 SITE 2 BC3 7 HOH H1087 ASP L 1A ALA L 1B SITE 1 BC4 2 ASN H 60G ACY H1004 CRYST1 83.766 134.017 44.033 90.00 90.00 90.00 P 21 21 2 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 0.011938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022710 0.00000