HEADER HYDROLASE 06-DEC-22 8BW5 TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA THROMBIN AND THE TITLE 2 DUPLEX/QUADRUPLEX APTAMER M08S-1_41MER 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 FRAGMENT: THROMBIN HEAVY CHAIN, UNP RESIDUES 364-622; COMPND 9 EC: 3.4.21.5; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: M08S-1_41MER; COMPND 12 CHAIN: F; 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: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS DNA APTAMER, G-QUADRUPLEX, DUPLEX, DUPLEX/QUADRUPLEX, THROMBIN KEYWDS 2 BINDING APTAMER, THROMBIN, COAGULATION FACTOR, ANTICOAGULANT, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.TROISI,V.NAPOLITANO,F.SICA REVDAT 3 20-SEP-23 8BW5 1 JRNL REVDAT 2 09-AUG-23 8BW5 1 JRNL REVDAT 1 19-JUL-23 8BW5 0 JRNL AUTH R.TROISI,V.NAPOLITANO,E.ROSSITTO,W.OSMAN,M.NAGANO,K.WAKUI, JRNL AUTH 2 G.M.POPOWICZ,K.YOSHIMOTO,F.SICA JRNL TITL STERIC HINDRANCE AND STRUCTURAL FLEXIBILITY SHAPE THE JRNL TITL 2 FUNCTIONAL PROPERTIES OF A GUANINE-RICH OLIGONUCLEOTIDE. JRNL REF NUCLEIC ACIDS RES. V. 51 8880 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37503836 JRNL DOI 10.1093/NAR/GKAD634 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14350 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 + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 721 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1036 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3830 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.4520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2342 REMARK 3 NUCLEIC ACID ATOMS : 846 REMARK 3 HETEROGEN ATOMS : 138 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -0.22000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.346 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.334 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.605 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3505 ; 0.003 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4935 ; 1.280 ; 1.709 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 288 ; 6.666 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 23 ; 4.953 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 429 ;15.795 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 539 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2307 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1161 ; 2.702 ; 5.658 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1446 ; 4.479 ; 8.484 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2344 ; 4.024 ; 8.912 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5700 ; 9.711 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292127209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15101 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 37.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000 20% W/V, MAGNESIUM ACETATE REMARK 280 0.2 M, SODIUM CACODYLATE 0.1 M, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 34.03000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.15500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.03000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.15500 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: 5090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, F, 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 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 -2 REMARK 465 PHE L -1 REMARK 465 GLY L 0 REMARK 465 GLY L 15 REMARK 465 ARG L 16 REMARK 465 DC F 41 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 DG F 9 C3' - O3' - P ANGL. DEV. = -7.8 DEGREES REMARK 500 DG F 14 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 DG F 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG F 23 C3' - O3' - P ANGL. DEV. = -9.0 DEGREES REMARK 500 DG F 27 O4' - C1' - N9 ANGL. DEV. = 2.7 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 7 -82.80 -127.09 REMARK 500 LYS L 9 0.29 -63.95 REMARK 500 ASN H 60G 87.73 -167.19 REMARK 500 HIS H 71 -63.87 -128.08 REMARK 500 ILE H 79 -54.11 -126.29 REMARK 500 GLU H 97A -71.27 -128.07 REMARK 500 ASN H 98 30.43 -143.42 REMARK 500 SER H 214 -75.51 -109.41 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 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221 O REMARK 620 2 LYS H 224 O 82.3 REMARK 620 3 HOH H 402 O 133.6 58.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA F 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG F 14 O6 REMARK 620 2 DG F 15 O6 71.0 REMARK 620 3 DG F 18 O6 123.6 63.8 REMARK 620 4 DG F 19 O6 70.2 102.8 88.3 REMARK 620 5 DG F 22 O6 115.8 163.3 117.1 93.9 REMARK 620 6 DG F 23 O6 159.9 99.1 62.3 129.7 69.3 REMARK 620 7 DG F 26 O6 96.6 59.5 88.4 161.4 103.9 63.6 REMARK 620 8 DG F 27 O6 60.2 100.7 156.7 113.0 72.5 106.4 68.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 630 REMARK 630 MOLECULE TYPE: NULL 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 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL DBREF 8BW5 L -2 16 UNP P00734 THRB_HUMAN 328 363 DBREF 8BW5 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 8BW5 F 1 41 PDB 8BW5 8BW5 1 41 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 F 41 DG DG DT DC DA DG DA DT DG DA DT DG DG SEQRES 2 F 41 DG DG DA DT DG DG DG DG DG DG DT DT DG SEQRES 3 F 41 DG DA DG DG DA DA DT DG DG DA DT DG DA SEQRES 4 F 41 DC DC HET NAG A 1 14 HET NAG A 2 14 HET BMA A 3 11 HET MAN A 4 11 HET NAG A 5 14 HET GAL A 6 11 HET SIA A 7 20 HET MAN A 8 11 HET 0G6 H 301 30 HET NA H 302 1 HET NA F 101 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID 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 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID HETSYN 0G6 PPACK FORMUL 4 NAG 3(C8 H15 N O6) FORMUL 4 BMA C6 H12 O6 FORMUL 4 MAN 2(C6 H12 O6) FORMUL 4 GAL C6 H12 O6 FORMUL 4 SIA C11 H19 N O9 FORMUL 5 0G6 C21 H34 CL N6 O3 1+ FORMUL 6 NA 2(NA 1+) FORMUL 8 HOH *21(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 GLU L 14C TYR L 14J 1 8 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 THR H 172 1 9 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 ASP H 243 1 10 SHEET 1 AA1 3 SER H 20 ASP H 21 0 SHEET 2 AA1 3 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 3 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 1 AA2 7 LYS H 81 SER H 83 0 SHEET 2 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 AA2 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 5 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 AA2 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 AA2 7 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SHEET 1 AA4 4 MET H 180 ALA H 183 0 SHEET 2 AA4 4 GLY H 226 HIS H 230 -1 O TYR H 228 N PHE H 181 SHEET 3 AA4 4 TRP H 207 TRP H 215 -1 N TRP H 215 O PHE H 227 SHEET 4 AA4 4 PRO H 198 LYS H 202 -1 N MET H 201 O TYR H 208 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.07 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 2.06 LINK NE2 HIS H 57 C3 0G6 H 301 1555 1555 1.42 LINK ND2 ASN H 60G C1 NAG A 1 1555 1555 1.43 LINK OG SER H 195 C2 0G6 H 301 1555 1555 1.43 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.44 LINK O6 BMA A 3 C1 MAN A 4 1555 1555 1.45 LINK O3 BMA A 3 C1 MAN A 8 1555 1555 1.46 LINK O2 MAN A 4 C1 NAG A 5 1555 1555 1.46 LINK O4 NAG A 5 C1 GAL A 6 1555 1555 1.46 LINK O6 GAL A 6 C2 SIA A 7 1555 1555 1.43 LINK O ARG H 221 NA NA H 302 1555 1555 2.68 LINK O LYS H 224 NA NA H 302 1555 1555 2.58 LINK NA NA H 302 O HOH H 402 1555 1555 2.39 LINK O6 DG F 14 NA NA F 101 1555 1555 2.60 LINK O6 DG F 15 NA NA F 101 1555 1555 2.62 LINK O6 DG F 18 NA NA F 101 1555 1555 2.59 LINK O6 DG F 19 NA NA F 101 1555 1555 2.32 LINK O6 DG F 22 NA NA F 101 1555 1555 2.21 LINK O6 DG F 23 NA NA F 101 1555 1555 2.95 LINK O6 DG F 26 NA NA F 101 1555 1555 2.81 LINK O6 DG F 27 NA NA F 101 1555 1555 2.77 CISPEP 1 SER H 36A PRO H 37 0 0.78 CRYST1 68.060 75.490 114.310 90.00 90.00 90.00 P 21 2 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 0.014693 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008748 0.00000