HEADER HYDROLASE 02-NOV-17 6EVV TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA THROMBIN AND NU172, TITLE 2 A DUPLEX/QUADRUPLEX 26-MER DNA APTAMER, IN THE PRESENCE OF POTASSIUM TITLE 3 IONS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTHROMBIN; COMPND 8 CHAIN: H; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: NU172, DNA (26-MER); COMPND 13 CHAIN: E; 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; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS THROMBIN-DNA, G-QUADRUPLEX, APTAMER, DUPLEX/QUADRUPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.TROISI,I.RUSSO KRAUSS,F.SICA REVDAT 6 17-JAN-24 6EVV 1 HETSYN LINK REVDAT 5 29-JUL-20 6EVV 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 27-MAR-19 6EVV 1 REMARK SITE REVDAT 3 26-DEC-18 6EVV 1 JRNL REVDAT 2 07-NOV-18 6EVV 1 JRNL REVDAT 1 24-OCT-18 6EVV 0 JRNL AUTH R.TROISI,V.NAPOLITANO,V.SPIRIDONOVA,I.RUSSO KRAUSS,F.SICA JRNL TITL SEVERAL STRUCTURAL MOTIFS COOPERATE IN DETERMINING THE JRNL TITL 2 HIGHLY EFFECTIVE ANTI-THROMBIN ACTIVITY OF NU172 APTAMER. JRNL REF NUCLEIC ACIDS RES. V. 46 12177 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30357392 JRNL DOI 10.1093/NAR/GKY990 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 104.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 25367 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1312 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1224 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2356 REMARK 3 NUCLEIC ACID ATOMS : 543 REMARK 3 HETEROGEN ATOMS : 144 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.80000 REMARK 3 B22 (A**2) : -2.99000 REMARK 3 B33 (A**2) : 6.79000 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): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.189 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.949 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3192 ; 0.008 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2710 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4445 ; 1.482 ; 1.837 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6292 ; 0.846 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 292 ; 2.748 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;25.335 ;23.217 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 436 ;11.171 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.243 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 461 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3103 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 716 ; 0.000 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): NULL ; NULL ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6EVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26684 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 93.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.31700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1PPB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TACSIMATE 50 % V/V, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.93750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.79750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 104.01700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.93750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.79750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 104.01700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.93750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.79750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 104.01700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.93750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.79750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 104.01700 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: 5860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, E, 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 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 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 498 O HOH H 504 1.83 REMARK 500 NH2 ARG H 187 OD1 ASP H 222 1.87 REMARK 500 NH2 ARG H 77A O4' DG E 20 1.96 REMARK 500 O THR H 149 O HOH H 401 2.16 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 -84.37 -135.25 REMARK 500 TYR H 60A 81.07 -152.46 REMARK 500 ASN H 60G 81.15 -171.91 REMARK 500 HIS H 71 -58.27 -136.31 REMARK 500 ILE H 79 -56.90 -122.12 REMARK 500 GLU H 97A -80.33 -113.22 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 86.9 REMARK 620 3 HOH H 437 O 112.4 160.6 REMARK 620 4 HOH H 444 O 153.2 66.7 93.9 REMARK 620 5 HOH H 458 O 85.3 88.3 91.8 89.3 REMARK 620 6 HOH H 486 O 96.7 79.8 98.5 83.6 167.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K E 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG E 7 O6 REMARK 620 2 DG E 8 O6 65.2 REMARK 620 3 DG E 11 O6 118.8 63.9 REMARK 620 4 DG E 12 O6 84.8 92.3 65.9 REMARK 620 5 DG E 16 O6 124.5 163.0 99.7 75.8 REMARK 620 6 DG E 17 O6 156.2 101.4 66.0 116.4 74.0 REMARK 620 7 DG E 20 O6 92.4 64.6 94.7 155.4 124.3 63.8 REMARK 620 8 DG E 21 O6 75.5 113.8 157.7 135.4 83.0 94.0 66.4 REMARK 620 N 1 2 3 4 5 6 7 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 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL DBREF 6EVV L 1H 14K UNP P00734 THRB_HUMAN 328 360 DBREF 6EVV H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 6EVV E 1 26 PDB 6EVV 6EVV 1 26 SEQADV 6EVV ASP L 15 UNP P00734 EXPRESSION TAG SEQADV 6EVV GLY L 16 UNP P00734 EXPRESSION TAG SEQADV 6EVV ARG L 17 UNP P00734 EXPRESSION TAG 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 E 26 DC DG DC DC DT DA DG DG DT DT DG DG DG SEQRES 2 E 26 DT DA DG DG DG DT DG DG DT DG DG DC DG 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 K E 101 1 HET GOL E 102 6 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 HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL 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 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL 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 NA 1+ FORMUL 7 K K 1+ FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *129(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 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 SER H 171 1 8 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 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O THR H 229 N ILE H 212 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 GLN H 30 ARG H 35 0 SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52 SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N TYR H 89 O LEU H 105 SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 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 SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.04 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.06 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 LINK NE2 HIS H 57 C3 0G6 H 301 1555 1555 1.46 LINK ND2 ASN H 60G C1 NAG A 1 1555 1555 1.44 LINK OG SER H 195 C2 0G6 H 301 1555 1555 1.42 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.45 LINK O4 NAG A 2 C1 BMA A 3 1555 1555 1.44 LINK O6 BMA A 3 C1 MAN A 4 1555 1555 1.44 LINK O3 BMA A 3 C1 MAN A 8 1555 1555 1.44 LINK O2 MAN A 4 C1 NAG A 5 1555 1555 1.44 LINK O4 NAG A 5 C1 GAL A 6 1555 1555 1.45 LINK O6 GAL A 6 C2 SIA A 7 1555 1555 1.34 LINK O ARG H 221 NA NA H 302 1555 1555 2.30 LINK O LYS H 224 NA NA H 302 1555 1555 2.51 LINK NA NA H 302 O HOH H 437 1555 1555 2.18 LINK NA NA H 302 O HOH H 444 1555 1555 2.47 LINK NA NA H 302 O HOH H 458 1555 1555 2.72 LINK NA NA H 302 O HOH H 486 1555 1555 2.24 LINK O6 DG E 7 K K E 101 1555 1555 2.68 LINK O6 DG E 8 K K E 101 1555 1555 2.96 LINK O6 DG E 11 K K E 101 1555 1555 2.76 LINK O6 DG E 12 K K E 101 1555 1555 2.57 LINK O6 DG E 16 K K E 101 1555 1555 2.55 LINK O6 DG E 17 K K E 101 1555 1555 3.00 LINK O6 DG E 20 K K E 101 1555 1555 2.83 LINK O6 DG E 21 K K E 101 1555 1555 2.74 CISPEP 1 SER H 36A PRO H 37 0 -1.06 CRYST1 67.875 113.595 208.034 90.00 90.00 90.00 I 2 2 2 8 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 0.014733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004807 0.00000