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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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