HEADER HYDROLASE 04-DEC-19 6V64 TITLE CRYSTAL STRUCTURE OF HUMAN THROMBIN BOUND TO PPACK WITH TRYPTOPHANS TITLE 2 REPLACED BY 5-F-TRYPTOPHAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 334-363; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 364-622; COMPND 12 SYNONYM: COAGULATION FACTOR II; COMPND 13 EC: 3.4.21.5; 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 GENE: F2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: F2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.A.RUBEN,Z.CHEN,E.DI CERA REVDAT 3 11-OCT-23 6V64 1 LINK REVDAT 2 24-JUN-20 6V64 1 JRNL REVDAT 1 13-MAY-20 6V64 0 JRNL AUTH E.A.RUBEN,P.S.GANDHI,Z.CHEN,S.K.KOESTER,G.T.DEKOSTER, JRNL AUTH 2 C.FRIEDEN,E.DI CERA JRNL TITL 19F NMR REVEALS THE CONFORMATIONAL PROPERTIES OF FREE JRNL TITL 2 THROMBIN AND ITS ZYMOGEN PRECURSOR PRETHROMBIN-2. JRNL REF J.BIOL.CHEM. V. 295 8227 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32358061 JRNL DOI 10.1074/JBC.RA120.013419 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.BODE,I.MAYR,U.BAUMANN,R.HUBER,S.R.STONE,J.HOFSTEENGE REMARK 1 TITL THE REFINED 1.9 A CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN: REMARK 1 TITL 2 INTERACTION WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE AND REMARK 1 TITL 3 SIGNIFICANCE OF THE TYR-PRO-PRO-TRP INSERTION SEGMENT. REMARK 1 REF EMBO J. V. 8 3467 1989 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 2583108 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 11333 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 588 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 636 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.4720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2283 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : 0.46000 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): 0.576 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.306 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.245 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.860 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2389 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2208 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3225 ; 1.766 ; 1.662 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5122 ; 1.938 ; 1.604 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 9.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;32.938 ;21.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;18.674 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.313 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 292 ; 0.249 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2628 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 533 ; 0.002 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 14 REMARK 3 ORIGIN FOR THE GROUP (A): 8.782 -3.912 -5.213 REMARK 3 T TENSOR REMARK 3 T11: 0.0943 T22: 0.1347 REMARK 3 T33: 0.0863 T12: 0.0323 REMARK 3 T13: -0.0023 T23: -0.0644 REMARK 3 L TENSOR REMARK 3 L11: 4.4453 L22: 4.2100 REMARK 3 L33: 9.5458 L12: -0.9632 REMARK 3 L13: 1.7475 L23: -1.1762 REMARK 3 S TENSOR REMARK 3 S11: -0.1099 S12: -0.5580 S13: 0.0187 REMARK 3 S21: 0.5751 S22: 0.1954 S23: -0.0956 REMARK 3 S31: -0.2671 S32: -0.1412 S33: -0.0855 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 16 B 245 REMARK 3 RESIDUE RANGE : A 101 A 101 REMARK 3 RESIDUE RANGE : B 301 B 302 REMARK 3 ORIGIN FOR THE GROUP (A): 18.332 -17.189 -15.174 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: 0.0407 REMARK 3 T33: 0.0423 T12: 0.0142 REMARK 3 T13: -0.0098 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 2.8060 L22: 2.8727 REMARK 3 L33: 2.2932 L12: -1.4207 REMARK 3 L13: -0.5753 L23: 0.3791 REMARK 3 S TENSOR REMARK 3 S11: -0.0977 S12: -0.2557 S13: -0.0903 REMARK 3 S21: 0.1316 S22: 0.0976 S23: -0.2331 REMARK 3 S31: 0.0824 S32: 0.2324 S33: 0.0001 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 4 REMARK 4 6V64 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245817. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12020 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 5.210 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33400 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 (%): 39.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NA/K TARTRATE PH 7.5 14% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 30.93450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.29950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.93450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.29950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 101 LIES ON A SPECIAL POSITION. 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 ARG A 15 REMARK 465 ALA B 148B REMARK 465 ASN B 148C REMARK 465 VAL B 148D REMARK 465 GLY B 148E REMARK 465 LYS B 148F REMARK 465 GLY B 246 REMARK 465 GLU B 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 ARG B 77A CG CD NE CZ NH1 NH2 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 OG SER B 195 C2 0G6 B 301 1.35 REMARK 500 NE2 HIS B 57 C3 0G6 B 301 1.50 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 -83.43 -121.52 REMARK 500 SER A 11 29.74 44.96 REMARK 500 ASP B 60E 64.45 25.70 REMARK 500 ASN B 60G 71.23 -160.03 REMARK 500 HIS B 71 -50.10 -124.87 REMARK 500 GLU B 77 69.47 -116.83 REMARK 500 GLU B 97A -85.98 -111.39 REMARK 500 THR B 147 -167.43 -161.11 REMARK 500 ASP B 186A 31.75 75.92 REMARK 500 SER B 214 -67.23 -120.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 0G6 B 301 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 A 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 14J O REMARK 620 2 TYR A 14J O 0.0 REMARK 620 3 HOH A 203 O 87.2 87.2 REMARK 620 4 HOH A 203 O 156.0 156.0 92.7 REMARK 620 5 TYR B 134 OH 84.3 84.3 103.0 72.3 REMARK 620 6 TYR B 134 OH 84.3 84.3 103.0 72.3 0.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 221A O REMARK 620 2 LYS B 224 O 87.1 REMARK 620 3 HOH B 406 O 116.1 156.2 REMARK 620 4 HOH B 427 O 75.5 80.0 99.8 REMARK 620 5 HOH B 434 O 152.9 67.5 88.7 90.3 REMARK 620 6 HOH B 462 O 107.9 84.3 92.9 163.8 79.9 REMARK 620 N 1 2 3 4 5 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 B 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0G6 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PPB RELATED DB: PDB DBREF 6V64 A 1B 15 UNP P00734 THRB_HUMAN 334 363 DBREF 6V64 B 16 247 UNP P00734 THRB_HUMAN 364 622 SEQRES 1 A 30 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 A 30 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 A 30 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 FTR 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 FTR VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO FTR 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 FTR 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 FTR GLY ASN SEQRES 12 B 259 LEU LYS GLU THR FTR 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 FTR TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER FTR 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 FTR ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU MODRES 6V64 FTR B 29 TRP MODIFIED RESIDUE MODRES 6V64 FTR B 51 TRP MODIFIED RESIDUE MODRES 6V64 FTR B 60D TRP MODIFIED RESIDUE MODRES 6V64 FTR B 96 TRP MODIFIED RESIDUE MODRES 6V64 FTR B 141 TRP MODIFIED RESIDUE MODRES 6V64 FTR B 148 TRP MODIFIED RESIDUE MODRES 6V64 FTR B 207 TRP MODIFIED RESIDUE MODRES 6V64 FTR B 215 TRP MODIFIED RESIDUE MODRES 6V64 FTR B 237 TRP MODIFIED RESIDUE HET FTR B 29 15 HET FTR B 51 15 HET FTR B 60D 15 HET FTR B 96 15 HET FTR B 141 15 HET FTR B 148 15 HET FTR B 207 15 HET FTR B 215 15 HET FTR B 237 15 HET NA A 101 1 HET 0G6 B 301 30 HET NA B 302 1 HETNAM FTR FLUOROTRYPTOPHANE HETNAM NA SODIUM ION 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 HETSYN 0G6 PPACK FORMUL 2 FTR 9(C11 H11 F N2 O2) FORMUL 3 NA 2(NA 1+) FORMUL 4 0G6 C21 H34 CL N6 O3 1+ FORMUL 6 HOH *108(H2 O) HELIX 1 AA1 PHE A 7 SER A 11 5 5 HELIX 2 AA2 GLU A 14C ASP A 14L 1 10 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 LEU B 234 ASP B 243 1 10 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 VAL B 138 O VAL B 158 SHEET 4 AA1 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 AA1 7 FTR B 207 FTR B 215 -1 O TYR B 208 N MET B 201 SHEET 6 AA1 7 GLY B 226 HIS B 230 -1 O PHE B 227 N FTR B 215 SHEET 7 AA1 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 AA2 7 GLN B 30 ARG B 35 0 SHEET 2 AA2 7 GLU B 39 LEU B 46 -1 O CYS B 42 N LEU B 33 SHEET 3 AA2 7 FTR B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 AA2 7 ALA B 104 LEU B 108 -1 O MET B 106 N VAL B 52 SHEET 5 AA2 7 LYS B 81 ILE B 90 -1 N TYR B 89 O LEU B 105 SHEET 6 AA2 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 7 AA2 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 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 SSBOND 1 CYS A 1 CYS B 122 1555 1555 1.92 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.12 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.05 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.09 LINK C PRO B 28 N FTR B 29 1555 1555 1.34 LINK C FTR B 29 N GLN B 30 1555 1555 1.34 LINK C ARG B 50 N FTR B 51 1555 1555 1.34 LINK C FTR B 51 N VAL B 52 1555 1555 1.34 LINK C PRO B 60C N FTR B 60D 1555 1555 1.34 LINK C FTR B 60D N ASP B 60E 1555 1555 1.34 LINK C ASN B 95 N FTR B 96 1555 1555 1.33 LINK C FTR B 96 N ARG B 97 1555 1555 1.34 LINK C GLY B 140 N FTR B 141 1555 1555 1.33 LINK C FTR B 141 N GLY B 142 1555 1555 1.34 LINK C THR B 147 N FTR B 148 1555 1555 1.32 LINK C FTR B 148 N THR B 148A 1555 1555 1.34 LINK C ARG B 206 N FTR B 207 1555 1555 1.33 LINK C FTR B 207 N TYR B 208 1555 1555 1.35 LINK C SER B 214 N FTR B 215 1555 1555 1.34 LINK C FTR B 215 N GLY B 216 1555 1555 1.34 LINK C LYS B 236 N FTR B 237 1555 1555 1.34 LINK C FTR B 237 N ILE B 238 1555 1555 1.33 LINK O TYR A 14J NA NA A 101 1555 1555 2.27 LINK O TYR A 14J NA NA A 101 1555 2555 2.28 LINK NA NA A 101 O HOH A 203 1555 1555 2.35 LINK NA NA A 101 O HOH A 203 1555 2555 2.37 LINK NA NA A 101 OH TYR B 134 1555 1555 2.62 LINK NA NA A 101 OH TYR B 134 2555 1555 2.59 LINK O ARG B 221A NA NA B 302 1555 1555 2.32 LINK O LYS B 224 NA NA B 302 1555 1555 2.32 LINK NA NA B 302 O HOH B 406 1555 1555 2.74 LINK NA NA B 302 O HOH B 427 1555 1555 2.65 LINK NA NA B 302 O HOH B 434 1555 1555 2.48 LINK NA NA B 302 O HOH B 462 1555 1555 2.39 CISPEP 1 SER B 36A PRO B 37 0 -5.92 SITE 1 AC1 3 TYR A 14J HOH A 203 TYR B 134 SITE 1 AC2 20 HIS B 57 TYR B 60A FTR B 60D GLU B 97A SITE 2 AC2 20 LEU B 99 ASP B 189 ALA B 190 GLY B 193 SITE 3 AC2 20 SER B 195 SER B 214 FTR B 215 GLY B 216 SITE 4 AC2 20 GLY B 219 CYS B 220 GLY B 226 LYS B 236 SITE 5 AC2 20 HOH B 405 HOH B 425 HOH B 435 HOH B 448 SITE 1 AC3 6 ARG B 221A LYS B 224 HOH B 406 HOH B 427 SITE 2 AC3 6 HOH B 434 HOH B 462 CRYST1 61.869 86.599 50.516 90.00 90.00 90.00 P 21 21 2 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016163 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019796 0.00000