HEADER HYDROLASE/HYDROLASE INHIBITOR/DNA 31-JUL-13 4LZ4 TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN THROMBIN AND THE TBA TITLE 2 DELETION MUTANT LACKING THYMINE 3 NUCLEOBASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 5 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN; COMPND 6 EC: 3.4.21.5; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 9 CHAIN: B, D; COMPND 10 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 11 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN HEAVY CHAIN; COMPND 12 EC: 3.4.21.5; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: THROMBIN BINDING APTAMER (TBA); COMPND 15 CHAIN: E, F; COMPND 16 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 OTHER_DETAILS: SYNTHETIC DNA KEYWDS PROTEIN-DNA COMPLEX, DNA APTAMER, G-QUADRUPLEX, TBA DELETION MUTANT, KEYWDS 2 SERINE PROTEASE, HYDROLASE, BLOOD COAGULATION, BLOOD, HYDROLASE-DNA KEYWDS 3 COMPLEX, HYDROLASE-HYDROLASE INHIBITOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PICA,I.RUSSO KRAUSS,A.MERLINO,F.SICA REVDAT 4 30-OCT-24 4LZ4 1 HETSYN REVDAT 3 29-JUL-20 4LZ4 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 15-NOV-17 4LZ4 1 REMARK REVDAT 1 08-JAN-14 4LZ4 0 JRNL AUTH A.PICA,I.RUSSO KRAUSS,A.MERLINO,S.NAGATOISHI,N.SUGIMOTO, JRNL AUTH 2 F.SICA JRNL TITL DISSECTING THE CONTRIBUTION OF THROMBIN EXOSITE I IN THE JRNL TITL 2 RECOGNITION OF THROMBIN BINDING APTAMER. JRNL REF FEBS J. V. 280 6581 2013 JRNL REFN ISSN 1742-464X JRNL PMID 24128303 JRNL DOI 10.1111/FEBS.12561 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 27048 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) : 0.168 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1430 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) : 2.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1664 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4708 REMARK 3 NUCLEIC ACID ATOMS : 612 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.508 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.279 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.342 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5620 ; 0.014 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 5007 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7738 ; 1.693 ; 1.864 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11538 ; 1.304 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 582 ; 6.893 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 229 ;32.734 ;23.362 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 859 ;16.200 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;15.003 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 783 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5845 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1281 ; 0.004 ; 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): 2340 ; 2.495 ; 3.323 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2341 ; 2.494 ; 3.322 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2915 ; 3.761 ; 4.984 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2916 ; 3.760 ; 4.983 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3280 ; 3.784 ; 4.183 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3279 ; 3.784 ; 4.183 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4823 ; 5.876 ; 6.167 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6988 ; 7.640 ;31.645 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6910 ; 7.572 ;31.653 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 : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 358 C 1 358 18702 0.08 0.05 REMARK 3 2 B 401 415 D 401 415 1235 0.11 0.05 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 REMARK 4 REMARK 4 4LZ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081263. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.009 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29590 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 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 (%) : 94.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60% TACSIMATE, 1-3% MPEG 5K OR PEG REMARK 280 8000, PH 7.0, VAPOR DIFFUSION, SITTING DROP, 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 60.36250 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 GLY A 15 REMARK 465 ARG A 16 REMARK 465 GLU B 247 REMARK 465 GLY C 15 REMARK 465 ARG C 16 REMARK 465 GLU D 247 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 E 1 C5' - C4' - O4' ANGL. DEV. = 11.2 DEGREES REMARK 500 DG F 1 C5' - C4' - O4' ANGL. DEV. = 10.1 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 A 7 -83.20 -131.27 REMARK 500 ALA B 44 170.19 178.86 REMARK 500 SER B 48 -163.53 -162.05 REMARK 500 ARG B 50 -0.60 -140.12 REMARK 500 ASN B 60G 79.83 -166.79 REMARK 500 HIS B 71 -53.73 -137.48 REMARK 500 ILE B 79 -64.47 -107.83 REMARK 500 GLU B 97A -80.33 -119.33 REMARK 500 PHE C 7 -81.79 -132.40 REMARK 500 ASN D 60G 82.21 -166.16 REMARK 500 HIS D 71 -52.94 -138.11 REMARK 500 ILE D 79 -65.58 -107.61 REMARK 500 GLU D 97A -79.22 -117.46 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 B 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 221 O REMARK 620 2 LYS B 224 O 92.0 REMARK 620 3 HOH B 443 O 85.0 92.0 REMARK 620 4 HOH B 446 O 101.4 166.1 85.6 REMARK 620 5 HOH B 452 O 98.4 88.3 176.5 93.2 REMARK 620 6 HOH B 482 O 167.7 78.0 88.0 88.2 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG D 221 O REMARK 620 2 LYS D 224 O 89.5 REMARK 620 3 HOH D 459 O 160.3 76.7 REMARK 620 4 HOH D 460 O 77.7 90.0 88.2 REMARK 620 5 HOH D 461 O 98.3 171.5 94.9 88.4 REMARK 620 N 1 2 3 4 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 1 O6 REMARK 620 2 DG E 2 O6 65.2 REMARK 620 3 DG E 5 O6 127.4 71.7 REMARK 620 4 DG E 6 O6 78.0 96.0 77.8 REMARK 620 5 DG E 10 O6 124.6 166.8 95.1 78.9 REMARK 620 6 DG E 11 O6 153.8 105.7 65.9 128.1 69.3 REMARK 620 7 DG E 14 O6 86.4 63.2 100.2 158.1 122.9 68.0 REMARK 620 8 DG E 15 O6 72.0 116.0 158.5 119.2 76.9 92.7 69.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K F 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG F 1 O6 REMARK 620 2 DG F 2 O6 67.6 REMARK 620 3 DG F 5 O6 122.9 70.9 REMARK 620 4 DG F 6 O6 72.3 90.6 70.6 REMARK 620 5 DG F 10 O6 118.2 162.9 93.6 76.9 REMARK 620 6 DG F 11 O6 165.3 111.0 67.9 122.3 67.7 REMARK 620 7 DG F 14 O6 93.0 66.6 104.8 156.6 126.5 73.7 REMARK 620 8 DG F 15 O6 76.4 120.5 160.7 121.6 76.4 92.9 70.0 REMARK 620 9 HOH F 201 O 119.8 56.1 57.0 123.9 121.9 55.3 47.9 114.4 REMARK 620 N 1 2 3 4 5 6 7 8 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 302 REMARK 630 0G6 D 302 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DIH RELATED DB: PDB REMARK 900 RELATED ID: 4DII RELATED DB: PDB REMARK 900 RELATED ID: 3QLP RELATED DB: PDB REMARK 900 RELATED ID: 4LZ1 RELATED DB: PDB DBREF 4LZ4 A 1H 16 UNP P00734 THRB_HUMAN 328 363 DBREF 4LZ4 B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 4LZ4 C 1H 16 UNP P00734 THRB_HUMAN 328 363 DBREF 4LZ4 D 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 4LZ4 E 1 15 PDB 4LZ4 4LZ4 1 15 DBREF 4LZ4 F 1 15 PDB 4LZ4 4LZ4 1 15 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 15 DG DG 3DR DT DG DG DT DG DT DG DG DT DT SEQRES 2 E 15 DG DG SEQRES 1 F 15 DG DG 3DR DT DG DG DT DG DT DG DG DT DT SEQRES 2 F 15 DG DG MODRES 4LZ4 ASN B 60G ASN GLYCOSYLATION SITE MODRES 4LZ4 ASN D 60G ASN GLYCOSYLATION SITE HET 3DR E 3 11 HET 3DR F 3 11 HET NAG B 301 14 HET 0G6 B 302 30 HET NA B 303 1 HET NAG D 301 14 HET 0G6 D 302 30 HET NA D 303 1 HET K E 101 1 HET K F 101 1 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 HETSYN 3DR ABASIC DIDEOXYRIBOSE 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 0G6 PPACK FORMUL 5 3DR 2(C5 H11 O6 P) FORMUL 7 NAG 2(C8 H15 N O6) FORMUL 8 0G6 2(C21 H34 CL N6 O3 1+) FORMUL 9 NA 2(NA 1+) FORMUL 13 K 2(K 1+) FORMUL 15 HOH *219(H2 O) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 THR A 14B TYR A 14J 1 9 HELIX 3 3 ALA B 55 LEU B 59 1 5 HELIX 4 4 PRO B 60B ASP B 60E 5 4 HELIX 5 5 THR B 60I ASN B 62 5 3 HELIX 6 6 ASP B 125 LEU B 130 1 9 HELIX 7 7 GLU B 164 THR B 172 1 9 HELIX 8 8 LYS B 185 GLY B 186C 5 5 HELIX 9 9 LEU B 234 ASP B 243 1 10 HELIX 10 10 GLY C 1D CYS C 1 5 5 HELIX 11 11 PHE C 7 SER C 11 5 5 HELIX 12 12 THR C 14B TYR C 14J 1 9 HELIX 13 13 ALA D 55 LEU D 59 1 5 HELIX 14 14 PRO D 60B ASP D 60E 5 4 HELIX 15 15 THR D 60I ASN D 62 5 3 HELIX 16 16 ASP D 125 LEU D 130 1 9 HELIX 17 17 GLU D 164 SER D 171 1 8 HELIX 18 18 LYS D 185 GLY D 186C 5 5 HELIX 19 19 VAL D 231 ASP D 243 1 13 SHEET 1 A 7 SER B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N VAL B 138 O VAL B 158 SHEET 4 A 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 A 7 TRP B 207 TRP B 215 -1 O GLY B 211 N PHE B 199 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O PHE B 227 N TRP B 215 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 GLN B 30 ARG B 35 0 SHEET 2 B 7 GLU B 39 LEU B 46 -1 O GLU B 39 N ARG B 35 SHEET 3 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 B 7 ALA B 104 LEU B 108 -1 O MET B 106 N VAL B 52 SHEET 5 B 7 LYS B 81 ILE B 90 -1 N TYR B 89 O LEU B 105 SHEET 6 B 7 LEU B 64 ILE B 68 -1 N VAL B 66 O SER B 83 SHEET 7 B 7 GLN B 30 ARG B 35 -1 N MET B 32 O ARG B 67 SHEET 1 C 2 LEU B 60 TYR B 60A 0 SHEET 2 C 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SHEET 1 D 7 SER D 20 ASP D 21 0 SHEET 2 D 7 GLN D 156 PRO D 161 -1 O VAL D 157 N SER D 20 SHEET 3 D 7 LYS D 135 GLY D 140 -1 N VAL D 138 O VAL D 158 SHEET 4 D 7 PRO D 198 LYS D 202 -1 O VAL D 200 N ARG D 137 SHEET 5 D 7 TRP D 207 TRP D 215 -1 O TYR D 208 N MET D 201 SHEET 6 D 7 GLY D 226 HIS D 230 -1 O THR D 229 N ILE D 212 SHEET 7 D 7 MET D 180 ALA D 183 -1 N PHE D 181 O TYR D 228 SHEET 1 E 7 GLN D 30 ARG D 35 0 SHEET 2 E 7 GLU D 39 LEU D 46 -1 O GLU D 39 N ARG D 35 SHEET 3 E 7 TRP D 51 THR D 54 -1 O LEU D 53 N SER D 45 SHEET 4 E 7 ALA D 104 LEU D 108 -1 O MET D 106 N VAL D 52 SHEET 5 E 7 LYS D 81 ILE D 90 -1 N TYR D 89 O LEU D 105 SHEET 6 E 7 LEU D 64 ILE D 68 -1 N ILE D 68 O LYS D 81 SHEET 7 E 7 GLN D 30 ARG D 35 -1 N MET D 32 O ARG D 67 SHEET 1 F 2 LEU D 60 TYR D 60A 0 SHEET 2 F 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 2.08 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.09 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.01 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.01 SSBOND 5 CYS C 1 CYS D 122 1555 1555 2.09 SSBOND 6 CYS D 42 CYS D 58 1555 1555 2.11 SSBOND 7 CYS D 168 CYS D 182 1555 1555 2.03 SSBOND 8 CYS D 191 CYS D 220 1555 1555 2.02 LINK NE2 HIS B 57 C3 0G6 B 302 1555 1555 1.49 LINK ND2 ASN B 60G C1 NAG B 301 1555 1555 1.43 LINK OG SER B 195 C2 0G6 B 302 1555 1555 1.42 LINK NE2 HIS D 57 C3 0G6 D 302 1555 1555 1.44 LINK ND2 ASN D 60G C1 NAG D 301 1555 1555 1.48 LINK OG SER D 195 C2 0G6 D 302 1555 1555 1.41 LINK O3' DG E 2 P 3DR E 3 1555 1555 1.61 LINK O3' 3DR E 3 P DT E 4 1555 1555 1.61 LINK O3' DG F 2 P 3DR F 3 1555 1555 1.60 LINK O3' 3DR F 3 P DT F 4 1555 1555 1.62 LINK O ARG B 221 NA NA B 303 1555 1555 2.30 LINK O LYS B 224 NA NA B 303 1555 1555 2.35 LINK NA NA B 303 O HOH B 443 1555 1555 2.97 LINK NA NA B 303 O HOH B 446 1555 1555 2.24 LINK NA NA B 303 O HOH B 452 1555 1555 2.33 LINK NA NA B 303 O HOH B 482 1555 1555 2.55 LINK O ARG D 221 NA NA D 303 1555 1555 2.36 LINK O LYS D 224 NA NA D 303 1555 1555 2.41 LINK NA NA D 303 O HOH D 459 1555 1555 2.33 LINK NA NA D 303 O HOH D 460 1555 1555 2.85 LINK NA NA D 303 O HOH D 461 1555 1555 2.35 LINK O6 DG E 1 K K E 101 1555 1555 2.72 LINK O6 DG E 2 K K E 101 1555 1555 2.93 LINK O6 DG E 5 K K E 101 1555 1555 2.71 LINK O6 DG E 6 K K E 101 1555 1555 2.48 LINK O6 DG E 10 K K E 101 1555 1555 2.62 LINK O6 DG E 11 K K E 101 1555 1555 3.15 LINK O6 DG E 14 K K E 101 1555 1555 2.92 LINK O6 DG E 15 K K E 101 1555 1555 2.75 LINK O6 DG F 1 K K F 101 1555 1555 2.60 LINK O6 DG F 2 K K F 101 1555 1555 2.86 LINK O6 DG F 5 K K F 101 1555 1555 2.79 LINK O6 DG F 6 K K F 101 1555 1555 2.79 LINK O6 DG F 10 K K F 101 1555 1555 2.64 LINK O6 DG F 11 K K F 101 1555 1555 2.96 LINK O6 DG F 14 K K F 101 1555 1555 2.73 LINK O6 DG F 15 K K F 101 1555 1555 2.86 LINK K K F 101 O HOH F 201 1555 1555 3.49 CISPEP 1 SER B 36A PRO B 37 0 -8.44 CISPEP 2 SER D 36A PRO D 37 0 -10.04 CRYST1 61.736 120.725 67.233 90.00 94.22 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 0.016198 0.000000 0.001195 0.00000 SCALE2 0.000000 0.008283 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014914 0.00000