HEADER HYDROLASE 10-MAR-21 7NTU TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA THROMBIN AND TWO TITLE 2 DUPLEX/QUADRUPLEX APTAMERS: NU172 AND HD22_27MER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A, C; 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: B, D; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: NU172; COMPND 13 CHAIN: E, G; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: HD22_27MER; COMPND 17 CHAIN: F, I; COMPND 18 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; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS TERNARY COMPLEX, ANTICOAGULANT APTAMERS, DUPLEX/QUADRUPLEX, KEYWDS 2 COAGULATION FACTOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.TROISI,A.SANTAMARIA,F.SICA REVDAT 3 31-JAN-24 7NTU 1 REMARK REVDAT 2 05-MAY-21 7NTU 1 JRNL REVDAT 1 28-APR-21 7NTU 0 JRNL AUTH R.TROISI,N.BALASCO,A.SANTAMARIA,L.VITAGLIANO,F.SICA JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE SIMULTANEOUS JRNL TITL 2 BINDING OF TWO DUPLEX/QUADRUPLEX APTAMERS TO HUMAN JRNL TITL 3 ALPHA-THROMBIN. JRNL REF INT.J.BIOL.MACROMOL. V. 181 858 2021 JRNL REFN ISSN 0141-8130 JRNL PMID 33864869 JRNL DOI 10.1016/J.IJBIOMAC.2021.04.076 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 20946 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1089 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1463 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4462 REMARK 3 NUCLEIC ACID ATOMS : 2214 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.73000 REMARK 3 B22 (A**2) : -4.28000 REMARK 3 B33 (A**2) : 2.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.67000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.466 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.383 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.771 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.840 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7243 ; 0.002 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5628 ; 0.000 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10305 ; 1.067 ; 1.474 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13057 ; 1.138 ; 1.925 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 548 ; 2.589 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 257 ;16.393 ;21.284 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 807 ;10.056 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ; 8.919 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 908 ; 0.050 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6581 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1677 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 4 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 6 33 C 6 33 757 0.140 0.050 REMARK 3 2 B 37 293 D 37 293 7450 0.140 0.050 REMARK 3 3 E 1 26 G 1 26 2602 0.100 0.050 REMARK 3 4 F 1 27 I 1 27 2640 0.100 0.050 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 7NTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : M 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 : 22065 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 60.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% W/V PEG 3350, 0.2 M AMMONIUM REMARK 280 ACETATE AND 0.1 M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 38.80800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, G, 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 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 A 1H REMARK 465 PHE A 1G REMARK 465 GLY A 1F REMARK 465 SER A 1E REMARK 465 GLY A 1D REMARK 465 ASP A 14L REMARK 465 GLY A 14M REMARK 465 ARG A 15 REMARK 465 THR B 146A REMARK 465 TRP B 146B REMARK 465 THR B 146C REMARK 465 ALA B 146D REMARK 465 ASN B 146E REMARK 465 VAL B 146F REMARK 465 GLY B 146G REMARK 465 LYS B 146H REMARK 465 GLY B 246 REMARK 465 GLU B 247 REMARK 465 THR C 1H REMARK 465 PHE C 1G REMARK 465 GLY C 1F REMARK 465 SER C 1E REMARK 465 GLY C 1D REMARK 465 ASP C 14L REMARK 465 GLY C 14M REMARK 465 ARG C 15 REMARK 465 THR D 146A REMARK 465 TRP D 146B REMARK 465 THR D 146C REMARK 465 ALA D 146D REMARK 465 ASN D 146E REMARK 465 VAL D 146F REMARK 465 GLY D 146G REMARK 465 LYS D 146H REMARK 465 GLY D 246 REMARK 465 GLU D 247 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 LYS A 10 CG CD CE NZ REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 LYS B 145 CG CD CE NZ REMARK 470 ARG B 173 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 1C CG CD OE1 OE2 REMARK 470 LYS D 110 CG CD CE NZ REMARK 470 LYS D 145 CG CD CE NZ REMARK 470 ARG D 173 CG CD NE CZ NH1 NH2 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 A 7 -99.22 -141.20 REMARK 500 GLN B 38 89.28 -66.93 REMARK 500 TYR B 60A 79.56 -150.95 REMARK 500 ASN B 60G 97.92 -166.21 REMARK 500 THR B 74 -61.78 -102.29 REMARK 500 ASN B 78 -3.61 65.00 REMARK 500 GLU B 97A -78.77 -85.05 REMARK 500 ALA B 104 137.43 -176.07 REMARK 500 SER B 115 -152.43 -140.48 REMARK 500 TRP B 141 36.60 -99.80 REMARK 500 ASP B 189 164.97 173.79 REMARK 500 PHE B 199 77.44 -111.17 REMARK 500 SER B 214 -81.46 -108.40 REMARK 500 PHE C 7 -98.22 -142.33 REMARK 500 GLN D 38 92.33 -64.32 REMARK 500 SER D 48 -174.51 -173.76 REMARK 500 TYR D 60A 79.01 -153.06 REMARK 500 ASN D 60G 89.87 -170.11 REMARK 500 HIS D 71 -46.14 -130.17 REMARK 500 THR D 74 -61.38 -102.34 REMARK 500 ASN D 78 -11.49 67.96 REMARK 500 ILE D 79 -64.94 -101.93 REMARK 500 GLU D 97A -79.12 -84.09 REMARK 500 ALA D 104 137.54 -175.99 REMARK 500 SER D 115 -154.62 -141.68 REMARK 500 TRP D 141 36.39 -99.36 REMARK 500 ASP D 189 167.38 178.42 REMARK 500 SER D 214 -81.43 -109.35 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 E 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG E 7 O6 REMARK 620 2 DG E 11 O6 116.7 REMARK 620 3 DG E 12 O6 86.3 65.6 REMARK 620 4 DG E 16 O6 139.0 89.4 76.4 REMARK 620 5 DG E 17 O6 146.9 62.7 118.4 72.1 REMARK 620 6 DG E 20 O6 85.5 91.9 149.0 126.8 61.9 REMARK 620 7 DG E 21 O6 78.9 151.6 142.1 92.4 91.1 64.6 REMARK 620 N 1 2 3 4 5 6 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 7 O6 REMARK 620 2 DG F 8 O6 73.2 REMARK 620 3 DG F 11 O6 105.7 88.5 REMARK 620 4 DG F 17 O6 138.9 147.4 86.8 REMARK 620 5 DG F 20 O6 89.2 90.1 164.0 85.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA G 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG G 7 O6 REMARK 620 2 DG G 11 O6 120.6 REMARK 620 3 DG G 12 O6 85.4 71.5 REMARK 620 4 DG G 16 O6 134.7 95.6 81.2 REMARK 620 5 DG G 17 O6 144.2 65.9 126.7 72.8 REMARK 620 6 DG G 20 O6 82.8 93.9 152.9 123.9 61.5 REMARK 620 7 DG G 21 O6 73.4 150.7 137.6 88.2 87.8 60.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA I 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG I 7 O6 REMARK 620 2 DG I 8 O6 70.6 REMARK 620 3 DG I 11 O6 90.3 74.8 REMARK 620 4 DG I 17 O6 141.5 141.7 83.2 REMARK 620 5 DG I 20 O6 95.9 96.8 167.3 98.5 REMARK 620 N 1 2 3 4 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 B 301 REMARK 630 0G6 D 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL DBREF 7NTU A 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 7NTU B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 7NTU C 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 7NTU D 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 7NTU E 1 26 PDB 7NTU 7NTU 1 26 DBREF 7NTU F 1 27 PDB 7NTU 7NTU 1 27 DBREF 7NTU G 1 26 PDB 7NTU 7NTU 1 26 DBREF 7NTU I 1 27 PDB 7NTU 7NTU 1 27 SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 A 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 C 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 C 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 C 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 D 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 D 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 D 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 D 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 D 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 D 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 D 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 D 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 D 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 D 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 D 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 D 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 D 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 D 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 D 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 D 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 D 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 D 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 D 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 D 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 SEQRES 1 F 27 DG DT DC DC DG DT DG DG DT DA DG DG DG SEQRES 2 F 27 DC DA DG DG DT DT DG DG DG DG DT DG DA SEQRES 3 F 27 DC SEQRES 1 G 26 DC DG DC DC DT DA DG DG DT DT DG DG DG SEQRES 2 G 26 DT DA DG DG DG DT DG DG DT DG DG DC DG SEQRES 1 I 27 DG DT DC DC DG DT DG DG DT DA DG DG DG SEQRES 2 I 27 DC DA DG DG DT DT DG DG DG DG DT DG DA SEQRES 3 I 27 DC HET 0G6 B 301 30 HET NAG B 302 14 HET 0G6 D 301 30 HET NAG D 302 14 HET NA E 101 1 HET NA F 101 1 HET NA G 101 1 HET NA I 101 1 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 NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETSYN 0G6 PPACK 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 9 0G6 2(C21 H34 CL N6 O3 1+) FORMUL 10 NAG 2(C8 H15 N O6) FORMUL 13 NA 4(NA 1+) FORMUL 17 HOH *53(H2 O) HELIX 1 AA1 PHE A 7 SER A 11 5 5 HELIX 2 AA2 THR A 14B GLU A 14H 1 7 HELIX 3 AA3 ALA B 55 CYS B 58 5 4 HELIX 4 AA4 PRO B 60B ASP B 60E 5 4 HELIX 5 AA5 THR B 60I ASN B 62 5 3 HELIX 6 AA6 ASP B 125 LEU B 130 1 9 HELIX 7 AA7 GLU B 164 SER B 171 1 8 HELIX 8 AA8 LYS B 185 GLY B 186C 5 5 HELIX 9 AA9 VAL B 231 PHE B 245 1 15 HELIX 10 AB1 PHE C 7 SER C 11 5 5 HELIX 11 AB2 THR C 14B SER C 14I 1 8 HELIX 12 AB3 ALA D 55 CYS D 58 5 4 HELIX 13 AB4 PRO D 60B ASP D 60E 5 4 HELIX 14 AB5 THR D 60I ASN D 62 5 3 HELIX 15 AB6 ASP D 125 LEU D 130 1 9 HELIX 16 AB7 GLU D 164 THR D 172 1 9 HELIX 17 AB8 LEU D 234 PHE D 245 1 12 SHEET 1 AA1 7 SER B 20 ASP B 21 0 SHEET 2 AA1 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 AA1 7 LYS B 135 GLY B 140 -1 N GLY B 136 O LEU B 160 SHEET 4 AA1 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 AA1 7 TRP B 207 TRP B 215 -1 O TYR B 208 N MET B 201 SHEET 6 AA1 7 GLY B 226 HIS B 230 -1 O THR B 229 N ILE B 212 SHEET 7 AA1 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 AA2 7 LYS B 81 SER B 83 0 SHEET 2 AA2 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 3 AA2 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 4 AA2 7 GLU B 39 LEU B 46 -1 O ALA B 44 N VAL B 31 SHEET 5 AA2 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 6 AA2 7 ALA B 104 LEU B 108 -1 O MET B 106 N VAL B 52 SHEET 7 AA2 7 LEU B 85 ILE B 90 -1 N GLU B 86 O LYS B 107 SHEET 1 AA3 2 LEU B 60 TYR B 60A 0 SHEET 2 AA3 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SHEET 1 AA4 7 SER D 20 ASP D 21 0 SHEET 2 AA4 7 GLN D 156 PRO D 161 -1 O VAL D 157 N SER D 20 SHEET 3 AA4 7 LYS D 135 GLY D 140 -1 N GLY D 136 O LEU D 160 SHEET 4 AA4 7 PRO D 198 LYS D 202 -1 O VAL D 200 N ARG D 137 SHEET 5 AA4 7 TRP D 207 TRP D 215 -1 O TYR D 208 N MET D 201 SHEET 6 AA4 7 GLY D 226 HIS D 230 -1 O THR D 229 N ILE D 212 SHEET 7 AA4 7 MET D 180 ALA D 183 -1 N PHE D 181 O TYR D 228 SHEET 1 AA5 7 LYS D 81 SER D 83 0 SHEET 2 AA5 7 LEU D 64 ILE D 68 -1 N ILE D 68 O LYS D 81 SHEET 3 AA5 7 GLN D 30 ARG D 35 -1 N PHE D 34 O LEU D 65 SHEET 4 AA5 7 GLU D 39 LEU D 46 -1 O ALA D 44 N VAL D 31 SHEET 5 AA5 7 TRP D 51 THR D 54 -1 O LEU D 53 N SER D 45 SHEET 6 AA5 7 ALA D 104 LEU D 108 -1 O MET D 106 N VAL D 52 SHEET 7 AA5 7 LEU D 85 ILE D 90 -1 N GLU D 86 O LYS D 107 SHEET 1 AA6 2 LEU D 60 TYR D 60A 0 SHEET 2 AA6 2 LYS D 60F ASN D 60G-1 O LYS D 60F N TYR D 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.04 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.05 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.03 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 SSBOND 5 CYS C 1 CYS D 122 1555 1555 2.04 SSBOND 6 CYS D 42 CYS D 58 1555 1555 2.04 SSBOND 7 CYS D 168 CYS D 182 1555 1555 2.03 SSBOND 8 CYS D 191 CYS D 220 1555 1555 2.03 LINK NE2 HIS B 57 C3 0G6 B 301 1555 1555 1.48 LINK ND2 ASN B 60G C1 NAG B 302 1555 1555 1.44 LINK OG SER B 195 C2 0G6 B 301 1555 1555 1.42 LINK NE2 HIS D 57 C3 0G6 D 301 1555 1555 1.47 LINK ND2 ASN D 60G C1 NAG D 302 1555 1555 1.44 LINK OG SER D 195 C2 0G6 D 301 1555 1555 1.43 LINK O6 DG E 7 NA NA E 101 1555 1555 2.66 LINK O6 DG E 11 NA NA E 101 1555 1555 3.13 LINK O6 DG E 12 NA NA E 101 1555 1555 2.74 LINK O6 DG E 16 NA NA E 101 1555 1555 2.61 LINK O6 DG E 17 NA NA E 101 1555 1555 3.18 LINK O6 DG E 20 NA NA E 101 1555 1555 3.03 LINK O6 DG E 21 NA NA E 101 1555 1555 2.69 LINK O6 DG F 7 NA NA F 101 1555 1555 2.95 LINK O6 DG F 8 NA NA F 101 1555 1555 2.48 LINK O6 DG F 11 NA NA F 101 1555 1555 2.30 LINK O6 DG F 17 NA NA F 101 1555 1555 2.78 LINK O6 DG F 20 NA NA F 101 1555 1555 2.64 LINK O6 DG G 7 NA NA G 101 1555 1555 2.86 LINK O6 DG G 11 NA NA G 101 1555 1555 2.90 LINK O6 DG G 12 NA NA G 101 1555 1555 2.53 LINK O6 DG G 16 NA NA G 101 1555 1555 2.60 LINK O6 DG G 17 NA NA G 101 1555 1555 3.14 LINK O6 DG G 20 NA NA G 101 1555 1555 3.10 LINK O6 DG G 21 NA NA G 101 1555 1555 2.87 LINK O6 DG I 7 NA NA I 101 1555 1555 3.00 LINK O6 DG I 8 NA NA I 101 1555 1555 2.62 LINK O6 DG I 11 NA NA I 101 1555 1555 2.52 LINK O6 DG I 17 NA NA I 101 1555 1555 2.77 LINK O6 DG I 20 NA NA I 101 1555 1555 2.12 CISPEP 1 SER B 36A PRO B 37 0 -0.74 CISPEP 2 SER D 36A PRO D 37 0 -1.01 CRYST1 84.927 77.616 95.408 90.00 103.47 90.00 P 1 21 1 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 0.011775 0.000000 0.002819 0.00000 SCALE2 0.000000 0.012884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010778 0.00000