HEADER LIGASE 03-OCT-25 9YJN TITLE TRYPANOSOMA CRUZI LYSYL-TRNA SYNTHETASE IN COMPLEX WITH L-LYSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSYL-TRNA SYNTHETASE; COMPND 5 EC: 6.1.1.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI DM28C; SOURCE 3 ORGANISM_TAXID: 1416333; SOURCE 4 GENE: TCDM_08178; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYSINE, TRNA, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR G.F.MERCALDI,A.T.CORDEIRO,M.FAGUNDES,E.H.S.BEZERRA,C.C.DE LIMA SILVA REVDAT 1 09-SEP-26 9YJN 0 JRNL AUTH T.C.F.DOS SANTOS,C.C.DE LIMA SILVA,A.G.EUFRAASIO, JRNL AUTH 2 C.TAMBASCIA,I.L.DE SOUSA,L.MARCHESE,M.F.CATELLI, JRNL AUTH 3 L.R.DE ALMEIDA,G.D.COSTA VENANCIO,V.B.DE SOUZA,A.A.SCHENKA, JRNL AUTH 4 S.A.ROCCO,G.F.MERCALDI,A.T.CORDEIRO JRNL TITL IN VIVO EFFICACY AND BIOCHEMICAL JRNL REF J.MED.CHEM. 2026 JRNL REFN ISSN 0022-2623 JRNL DOI 10.1021/ACS.JMEDCHEM.6C00764 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0415 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 33768 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1780 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) : 2.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2384 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3955 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.00000 REMARK 3 B22 (A**2) : 1.00000 REMARK 3 B33 (A**2) : -1.99000 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): 0.195 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.989 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4057 ; 0.014 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3843 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5486 ; 2.116 ; 1.662 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8837 ; 0.692 ; 1.575 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 484 ; 7.870 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;10.757 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 705 ;16.511 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 595 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4784 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 980 ; 0.001 ; 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): 1948 ; 5.831 ; 4.193 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1948 ; 5.831 ; 4.193 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2428 ; 7.684 ; 7.504 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2429 ; 7.682 ; 7.504 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2109 ; 7.059 ; 4.711 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2110 ; 7.057 ; 4.710 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3059 ; 9.592 ; 8.395 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4406 ;11.793 ;41.840 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4396 ;11.803 ;41.840 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 : 1 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 58 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): -1.1014 -17.2213 4.4249 REMARK 3 T TENSOR REMARK 3 T11: 0.0613 T22: 0.0364 REMARK 3 T33: 0.1097 T12: 0.0252 REMARK 3 T13: 0.0225 T23: 0.0386 REMARK 3 L TENSOR REMARK 3 L11: 0.6841 L22: 1.2303 REMARK 3 L33: 1.6976 L12: -0.1738 REMARK 3 L13: -0.2973 L23: 0.5989 REMARK 3 S TENSOR REMARK 3 S11: -0.0859 S12: -0.1447 S13: -0.2372 REMARK 3 S21: 0.1571 S22: 0.0338 S23: 0.0384 REMARK 3 S31: 0.3132 S32: 0.1113 S33: 0.0521 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 9YJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000297979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS SIRIUS REMARK 200 BEAMLINE : MANACA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9772 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35668 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 47.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.460 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 25.10 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 24.80 REMARK 200 R MERGE FOR SHELL (I) : 2.99900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5; 0.4 M SODIUM REMARK 280 ACETATE; 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 155.16900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.98350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.98350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 232.75350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.98350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.98350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.58450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.98350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.98350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 232.75350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.98350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.98350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 77.58450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 155.16900 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: 8810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 GLU A 6 REMARK 465 THR A 7 REMARK 465 ARG A 8 REMARK 465 ALA A 9 REMARK 465 GLN A 10 REMARK 465 ILE A 11 REMARK 465 ASP A 12 REMARK 465 ASP A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 ILE A 18 REMARK 465 ALA A 19 REMARK 465 GLN A 20 REMARK 465 VAL A 21 REMARK 465 LYS A 22 REMARK 465 LYS A 23 REMARK 465 GLU A 24 REMARK 465 LYS A 25 REMARK 465 GLY A 26 REMARK 465 ALA A 27 REMARK 465 ALA A 28 REMARK 465 SER A 29 REMARK 465 GLU A 30 REMARK 465 GLU A 31 REMARK 465 CYS A 32 REMARK 465 ARG A 33 REMARK 465 ALA A 34 REMARK 465 LEU A 35 REMARK 465 VAL A 36 REMARK 465 ALA A 37 REMARK 465 GLU A 38 REMARK 465 MET A 39 REMARK 465 THR A 40 REMARK 465 GLU A 41 REMARK 465 LEU A 42 REMARK 465 ARG A 43 REMARK 465 LYS A 44 REMARK 465 GLN A 45 REMARK 465 LEU A 46 REMARK 465 PRO A 47 REMARK 465 ALA A 48 REMARK 465 LYS A 49 REMARK 465 LYS A 50 REMARK 465 VAL A 51 REMARK 465 GLU A 52 REMARK 465 LYS A 53 REMARK 465 ALA A 54 REMARK 465 PRO A 55 REMARK 465 GLU A 56 REMARK 465 LEU A 57 REMARK 465 GLY A 198 REMARK 465 TRP A 199 REMARK 465 TYR A 200 REMARK 465 GLY A 201 REMARK 465 LEU A 202 REMARK 465 SER A 203 REMARK 465 ASP A 359 REMARK 465 SER A 360 REMARK 465 GLU A 361 REMARK 465 GLY A 362 REMARK 465 ASN A 363 REMARK 465 GLN A 364 REMARK 465 LYS A 557 REMARK 465 PRO A 558 REMARK 465 GLU A 559 REMARK 465 THR A 560 REMARK 465 SER A 561 REMARK 465 SER A 562 REMARK 465 SER A 563 REMARK 465 LEU A 564 REMARK 465 THR A 565 REMARK 465 TYR A 566 REMARK 465 PRO A 567 REMARK 465 PRO A 568 REMARK 465 GLY A 569 REMARK 465 THR A 570 REMARK 465 LEU A 571 REMARK 465 LEU A 572 REMARK 465 ASN A 573 REMARK 465 GLY A 574 REMARK 465 GLN A 575 REMARK 465 GLY A 576 REMARK 465 VAL A 577 REMARK 465 PRO A 578 REMARK 465 LEU A 579 REMARK 465 LEU A 580 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 295 CG ASP A 295 OD1 0.139 REMARK 500 GLU A 299 CD GLU A 299 OE2 0.092 REMARK 500 GLU A 396 CD GLU A 396 OE1 0.067 REMARK 500 GLU A 494 CD GLU A 494 OE1 0.073 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 210 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 210 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 TYR A 298 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 298 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 378 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 378 NE - CZ - NH2 ANGL. DEV. = -5.1 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 TYR A 146 158.39 -48.12 REMARK 500 SER A 173 159.05 -40.85 REMARK 500 GLU A 307 -146.60 -137.74 REMARK 500 ASP A 310 -137.37 -129.95 REMARK 500 TYR A 326 7.31 81.17 REMARK 500 GLU A 436 115.67 -22.92 REMARK 500 PRO A 437 150.87 -43.58 REMARK 500 ASP A 447 54.69 76.59 REMARK 500 ASP A 462 103.67 -172.17 REMARK 500 ALA A 509 152.06 -45.30 REMARK 500 ALA A 523 100.85 90.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 208 0.10 SIDE CHAIN REMARK 500 ARG A 229 0.11 SIDE CHAIN REMARK 500 ARG A 305 0.09 SIDE CHAIN REMARK 500 ARG A 378 0.11 SIDE CHAIN REMARK 500 ARG A 407 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9YJN A 1 580 UNP V5ASS1 V5ASS1_TRYCR 1 580 SEQADV 9YJN ASN A 461 UNP V5ASS1 ASP 461 CONFLICT SEQRES 1 A 580 MET SER SER THR ASN GLU THR ARG ALA GLN ILE ASP ASP SEQRES 2 A 580 LEU ALA ALA ALA ILE ALA GLN VAL LYS LYS GLU LYS GLY SEQRES 3 A 580 ALA ALA SER GLU GLU CYS ARG ALA LEU VAL ALA GLU MET SEQRES 4 A 580 THR GLU LEU ARG LYS GLN LEU PRO ALA LYS LYS VAL GLU SEQRES 5 A 580 LYS ALA PRO GLU LEU SER TYR PHE ASP THR ARG LEU ALA SEQRES 6 A 580 MET VAL LYS GLU LEU GLY LEU LEU GLY ALA ALA TYR PRO SEQRES 7 A 580 HIS LYS PHE ASP ARG GLN TYR THR ILE PRO ALA PHE LYS SEQRES 8 A 580 ALA ARG PHE ALA PRO GLN LEU SER GLU LYS GLY GLN ARG SEQRES 9 A 580 VAL GLU GLU VAL VAL ALA ILE ALA GLY ARG ILE VAL ASN SEQRES 10 A 580 LYS ARG SER SER GLY SER LYS LEU ASN PHE LEU THR LEU SEQRES 11 A 580 GLN GLY ASP ALA ASP THR VAL GLN VAL ILE SER ALA ILE SEQRES 12 A 580 SER ASP TYR VAL ASP ASP THR PHE ALA ALA VAL HIS GLY SEQRES 13 A 580 ARG ILE ARG ARG GLY ASP ILE ILE GLY VAL LYS GLY VAL SEQRES 14 A 580 ALA SER LEU SER LYS THR GLY GLU PHE SER MET ASN ALA SEQRES 15 A 580 PHE GLU ILE THR LEU LEU SER THR CYS TYR HIS MET LEU SEQRES 16 A 580 PRO ASP GLY TRP TYR GLY LEU SER SER ILE GLU GLN ARG SEQRES 17 A 580 PHE ARG GLN ARG TYR LEU ASP PHE ILE VAL ASN ARG GLU SEQRES 18 A 580 ASN ILE GLN THR PHE VAL THR ARG SER LYS VAL ILE ARG SEQRES 19 A 580 TYR ILE ARG ASN PHE PHE GLU ASP LEU ASP PHE LEU GLU SEQRES 20 A 580 VAL GLU THR PRO VAL LEU ASN GLN ILE ALA GLY GLY ALA SEQRES 21 A 580 ALA ALA ARG PRO PHE ILE THR HIS HIS ASN GLU LEU ASN SEQRES 22 A 580 GLN ARG MET TYR LEU ARG ILE ALA PRO GLU LEU TYR LEU SEQRES 23 A 580 LYS GLU LEU VAL VAL GLY GLY MET ASP ARG VAL TYR GLU SEQRES 24 A 580 LEU GLY LYS GLN PHE ARG ASN GLU GLY ILE ASP LEU THR SEQRES 25 A 580 HIS ASN PRO GLU PHE THR SER VAL GLU ALA TYR TRP ALA SEQRES 26 A 580 TYR ALA ASP TYR ASN ASP TRP MET ARG THR THR GLU ASP SEQRES 27 A 580 LEU PHE TYR GLY LEU ALA MET HIS ILE HIS GLY THR PRO SEQRES 28 A 580 PHE VAL LYS TYR ALA PRO LYS ASP SER GLU GLY ASN GLN SEQRES 29 A 580 LEU PRO GLU VAL VAL PHE ASN PHE ASN LYS PRO PHE LYS SEQRES 30 A 580 ARG LEU TYR ILE ILE PRO GLU LEU GLU LYS ARG MET ASN SEQRES 31 A 580 VAL LYS PHE PRO THR GLU PHE GLU SER ASP SER SER ASN SEQRES 32 A 580 ALA PHE LEU ARG GLU LEU CYS SER LYS HIS GLU VAL GLU SEQRES 33 A 580 CYS ILE PRO PRO LEU THR THR ALA ARG LEU LEU ASP ALA SEQRES 34 A 580 LEU ILE SER HIS TYR LEU GLU PRO GLU CYS GLN ASP PRO SEQRES 35 A 580 THR PHE VAL CYS ASP HIS PRO ARG VAL MET SER PRO LEU SEQRES 36 A 580 ALA LYS TRP HIS ARG ASN ASP PRO GLN LEU THR GLU ARG SEQRES 37 A 580 PHE GLU LEU PHE LEU ASN LYS LYS GLU LEU CYS ASN ALA SEQRES 38 A 580 TYR THR GLU LEU ASN ASN PRO ILE VAL GLN ARG GLU GLU SEQRES 39 A 580 PHE MET LYS GLN LEU ARG ASN LYS GLU LYS GLY ASP ASP SEQRES 40 A 580 GLU ALA MET ASP ILE ASP GLU GLY PHE VAL GLN ALA LEU SEQRES 41 A 580 GLU HIS ALA LEU PRO PRO THR GLY GLY TRP GLY LEU GLY SEQRES 42 A 580 ILE ASP ARG LEU VAL MET PHE LEU THR SER GLN ALA ASN SEQRES 43 A 580 ILE LYS GLU VAL LEU LEU PHE PRO ALA MET LYS PRO GLU SEQRES 44 A 580 THR SER SER SER LEU THR TYR PRO PRO GLY THR LEU LEU SEQRES 45 A 580 ASN GLY GLN GLY VAL PRO LEU LEU HET LYS A 601 10 HETNAM LYS LYSINE FORMUL 2 LYS C6 H15 N2 O2 1+ FORMUL 3 HOH *66(H2 O) HELIX 1 AA1 SER A 58 LEU A 72 1 15 HELIX 2 AA2 THR A 86 ALA A 95 1 10 HELIX 3 AA3 PRO A 96 LEU A 98 5 3 HELIX 4 AA4 THR A 150 ILE A 158 1 9 HELIX 5 AA5 ILE A 205 GLN A 211 1 7 HELIX 6 AA6 GLN A 211 ASN A 219 1 9 HELIX 7 AA7 ASN A 222 LEU A 243 1 22 HELIX 8 AA8 PRO A 282 GLY A 292 1 11 HELIX 9 AA9 ASP A 328 HIS A 348 1 21 HELIX 10 AB1 ILE A 381 ASN A 390 1 10 HELIX 11 AB2 SER A 399 HIS A 413 1 15 HELIX 12 AB3 THR A 422 TYR A 434 1 13 HELIX 13 AB4 PRO A 449 SER A 453 5 5 HELIX 14 AB5 ASN A 487 LYS A 504 1 18 HELIX 15 AB6 ASP A 513 GLU A 521 1 9 HELIX 16 AB7 ILE A 534 THR A 542 1 9 HELIX 17 AB8 ASN A 546 LEU A 551 5 6 SHEET 1 AA1 6 ARG A 104 SER A 120 0 SHEET 2 AA1 6 LEU A 125 GLY A 132 -1 O THR A 129 N ASN A 117 SHEET 3 AA1 6 ASP A 135 ALA A 142 -1 O SER A 141 N ASN A 126 SHEET 4 AA1 6 PHE A 178 SER A 189 1 O ALA A 182 N ILE A 140 SHEET 5 AA1 6 ILE A 163 LEU A 172 -1 N LYS A 167 O PHE A 183 SHEET 6 AA1 6 ARG A 104 SER A 120 -1 N ILE A 111 O VAL A 166 SHEET 1 AA2 8 LEU A 246 GLU A 247 0 SHEET 2 AA2 8 ARG A 296 PHE A 304 1 O ARG A 296 N LEU A 246 SHEET 3 AA2 8 GLU A 316 ALA A 325 -1 O PHE A 317 N GLN A 303 SHEET 4 AA2 8 THR A 527 GLY A 533 -1 O GLY A 528 N TRP A 324 SHEET 5 AA2 8 LYS A 476 THR A 483 -1 N TYR A 482 O GLY A 529 SHEET 6 AA2 8 ARG A 468 LEU A 473 -1 N LEU A 471 O LEU A 478 SHEET 7 AA2 8 THR A 443 CYS A 446 -1 N VAL A 445 O GLU A 470 SHEET 8 AA2 8 LYS A 377 TYR A 380 1 N LYS A 377 O PHE A 444 SHEET 1 AA3 3 LEU A 253 ASN A 254 0 SHEET 2 AA3 3 GLN A 274 LEU A 278 -1 O TYR A 277 N ASN A 254 SHEET 3 AA3 3 ILE A 266 HIS A 269 -1 N THR A 267 O MET A 276 SHEET 1 AA4 2 PHE A 352 TYR A 355 0 SHEET 2 AA4 2 VAL A 368 ASN A 371 -1 O VAL A 368 N TYR A 355 SHEET 1 AA5 2 TRP A 458 HIS A 459 0 SHEET 2 AA5 2 ASP A 462 THR A 466 -1 O LEU A 465 N HIS A 459 SSBOND 1 CYS A 410 CYS A 417 1555 1555 2.55 CISPEP 1 LYS A 374 PRO A 375 0 -2.97 CISPEP 2 PRO A 419 PRO A 420 0 -4.43 CRYST1 59.967 59.967 310.338 90.00 90.00 90.00 P 43 21 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 0.016676 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003222 0.00000 CONECT 2778 2834 CONECT 2834 2778 MASTER 471 0 1 17 21 0 0 6 4031 1 2 45 END