HEADER IMMUNE SYSTEM 23-NOV-19 6LDX TITLE STRUCTURE ANTIBODY E6 IN COMPLEX WITH METHYLATED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: GLY-M3L-GLY-GLY-THR-TYR-PRO; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_TAXID: 9986; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL: 293; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 9 ORGANISM_TAXID: 9986; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL: 293; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606 KEYWDS METHYLATION; ANTIBODY; PHAGE DISPLAY; BIOMOLECULAR RECOGNITION, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,K.TSUMOTO REVDAT 4 22-NOV-23 6LDX 1 REMARK REVDAT 3 14-JUL-21 6LDX 1 JRNL REVDAT 2 23-DEC-20 6LDX 1 JRNL REVDAT 1 25-NOV-20 6LDX 0 JRNL AUTH M.ISHII,M.NAKAKIDO,J.M.M.CAAVEIRO,D.KURODA,C.J.OKUMURA, JRNL AUTH 2 T.MARUYAMA,K.ENTZMINGER,K.TSUMOTO JRNL TITL STRUCTURAL BASIS FOR ANTIGEN RECOGNITION BY METHYLATED JRNL TITL 2 LYSINE-SPECIFIC ANTIBODIES. JRNL REF J.BIOL.CHEM. V. 296 00176 2020 JRNL REFN ESSN 1083-351X JRNL PMID 33303630 JRNL DOI 10.1074/JBC.RA120.015996 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 37400 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1562 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2675 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3223 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.25000 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): 0.122 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.958 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3346 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2935 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4604 ; 1.857 ; 1.659 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6869 ; 1.483 ; 1.564 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 444 ; 7.445 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;36.410 ;23.721 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;12.907 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.676 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 474 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3774 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 653 ; 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): 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 : 3 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 : H -1 H 212 REMARK 3 ORIGIN FOR THE GROUP (A): 3.4039 16.3512 13.6609 REMARK 3 T TENSOR REMARK 3 T11: 0.0701 T22: 0.0072 REMARK 3 T33: 0.0249 T12: -0.0057 REMARK 3 T13: 0.0069 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 2.4080 L22: 0.4496 REMARK 3 L33: 0.5100 L12: -0.3997 REMARK 3 L13: 0.0180 L23: -0.1218 REMARK 3 S TENSOR REMARK 3 S11: 0.0418 S12: -0.1010 S13: 0.0069 REMARK 3 S21: 0.0137 S22: -0.0017 S23: 0.0050 REMARK 3 S31: -0.0747 S32: -0.0068 S33: -0.0401 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 214 REMARK 3 ORIGIN FOR THE GROUP (A): 2.3027 -1.1610 16.8300 REMARK 3 T TENSOR REMARK 3 T11: 0.0808 T22: 0.0260 REMARK 3 T33: 0.0285 T12: 0.0025 REMARK 3 T13: -0.0031 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.8810 L22: 0.5731 REMARK 3 L33: 0.2493 L12: -0.3309 REMARK 3 L13: 0.0804 L23: -0.0913 REMARK 3 S TENSOR REMARK 3 S11: 0.0467 S12: 0.0885 S13: -0.1386 REMARK 3 S21: 0.0021 S22: -0.0327 S23: 0.0657 REMARK 3 S31: -0.0140 S32: -0.0072 S33: -0.0140 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 14 REMARK 3 ORIGIN FOR THE GROUP (A): -23.1569 16.8635 5.0135 REMARK 3 T TENSOR REMARK 3 T11: 0.0592 T22: 0.0758 REMARK 3 T33: 0.1312 T12: 0.0292 REMARK 3 T13: -0.0355 T23: 0.0319 REMARK 3 L TENSOR REMARK 3 L11: 2.7607 L22: 3.9906 REMARK 3 L33: 7.8190 L12: 0.7064 REMARK 3 L13: -0.9411 L23: -0.0371 REMARK 3 S TENSOR REMARK 3 S11: 0.2054 S12: 0.1521 S13: -0.0236 REMARK 3 S21: 0.0630 S22: 0.0197 S23: 0.1597 REMARK 3 S31: -0.2365 S32: -0.0997 S33: -0.2251 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REMARK 3 WITH TLS ADDED REMARK 3 REMARK 3 SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS REMARK 3 COLUMNS. REMARK 4 REMARK 4 6LDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39032 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 67.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 23.20 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.46800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 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: 6LDV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM CHLORIDE 24% PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 60.13450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.16450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.16450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.06725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.16450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.16450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.20175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.16450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.16450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.06725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.16450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.16450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.20175 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 60.13450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, 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 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 H 213 REMARK 465 CYS H 214 REMARK 465 SER H 215 REMARK 465 LYS H 216 REMARK 465 PRO H 217 REMARK 465 ALA H 218 REMARK 465 ALA H 219 REMARK 465 ALA H 220 REMARK 465 GLU H 221 REMARK 465 GLN H 222 REMARK 465 LYS H 223 REMARK 465 LEU H 224 REMARK 465 ILE H 225 REMARK 465 SER H 226 REMARK 465 GLU H 227 REMARK 465 GLU H 228 REMARK 465 ASP H 229 REMARK 465 LEU H 230 REMARK 465 ASN H 231 REMARK 465 SER H 232 REMARK 465 ALA H 233 REMARK 465 VAL H 234 REMARK 465 ASP H 235 REMARK 465 HIS H 236 REMARK 465 HIS H 237 REMARK 465 HIS H 238 REMARK 465 HIS H 239 REMARK 465 HIS H 240 REMARK 465 HIS H 241 REMARK 465 ALA L 215 REMARK 465 ALA L 216 REMARK 465 ALA L 217 REMARK 465 GLU L 218 REMARK 465 GLN L 219 REMARK 465 LYS L 220 REMARK 465 LEU L 221 REMARK 465 ILE L 222 REMARK 465 SER L 223 REMARK 465 GLU L 224 REMARK 465 GLU L 225 REMARK 465 ASP L 226 REMARK 465 LEU L 227 REMARK 465 ASN L 228 REMARK 465 SER L 229 REMARK 465 ALA L 230 REMARK 465 VAL L 231 REMARK 465 ASP L 232 REMARK 465 HIS L 233 REMARK 465 HIS L 234 REMARK 465 HIS L 235 REMARK 465 HIS L 236 REMARK 465 HIS L 237 REMARK 465 HIS L 238 REMARK 465 ASN B 1 REMARK 465 PRO B 2 REMARK 465 ILE B 3 REMARK 465 PHE B 4 REMARK 465 GLU B 5 REMARK 465 LYS B 6 REMARK 465 PHE B 7 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 GLU L 162 CD GLU L 162 OE1 0.067 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 THR H 71 -162.34 -105.00 REMARK 500 TYR H 99 32.49 70.04 REMARK 500 ASN L 31 18.06 57.74 REMARK 500 ASN L 32 -1.57 66.25 REMARK 500 ALA L 53 -31.94 73.49 REMARK 500 SER L 54 -5.87 -141.87 REMARK 500 ALA L 86 173.70 176.94 REMARK 500 LYS L 141 85.08 53.29 REMARK 500 CYS L 173 -1.34 78.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL H 301 DBREF 6LDX H -1 241 PDB 6LDX 6LDX -1 241 DBREF 6LDX L 1 238 PDB 6LDX 6LDX 1 238 DBREF 6LDX B 1 14 PDB 6LDX 6LDX 1 14 SEQRES 1 H 243 GLY ASP GLN SER LEU GLU GLU SER GLY GLY ARG LEU VAL SEQRES 2 H 243 THR PRO GLY THR PRO LEU THR LEU THR CYS THR VAL SER SEQRES 3 H 243 GLY PHE SER LEU ASN ASN ASN ALA MET GLY TRP PHE ARG SEQRES 4 H 243 GLN ALA PRO GLY GLU GLY LEU GLU TRP ILE GLY ALA ILE SEQRES 5 H 243 TYR THR ASP GLY SER THR TYR TYR ALA SER TRP ALA LYS SEQRES 6 H 243 GLY ARG PHE THR ILE SER LYS THR SER THR THR ILE ASP SEQRES 7 H 243 LEU LYS MET THR SER LEU THR THR GLU ASP THR ALA THR SEQRES 8 H 243 TYR PHE CYS ALA ARG HIS GLY TYR THR TYR SER PHE ASN SEQRES 9 H 243 LEU TRP GLY PRO GLY THR LEU VAL THR VAL SER SER GLY SEQRES 10 H 243 GLN PRO LYS ALA PRO SER VAL PHE PRO LEU ALA PRO CYS SEQRES 11 H 243 CYS GLY ASP THR PRO SER SER THR VAL THR LEU GLY CYS SEQRES 12 H 243 LEU VAL LYS GLY TYR LEU PRO GLU PRO VAL THR VAL THR SEQRES 13 H 243 TRP ASN SER GLY THR LEU THR ASN GLY VAL ARG THR PHE SEQRES 14 H 243 PRO SER VAL ARG GLN SER SER GLY LEU TYR SER LEU SER SEQRES 15 H 243 SER VAL VAL SER VAL THR SER SER SER GLN PRO VAL THR SEQRES 16 H 243 CYS ASN VAL ALA HIS PRO ALA THR ASN THR LYS VAL ASP SEQRES 17 H 243 LYS THR VAL ALA PRO SER THR CYS SER LYS PRO ALA ALA SEQRES 18 H 243 ALA GLU GLN LYS LEU ILE SER GLU GLU ASP LEU ASN SER SEQRES 19 H 243 ALA VAL ASP HIS HIS HIS HIS HIS HIS SEQRES 1 L 238 ASP PRO VAL MET THR GLN THR PRO PRO SER VAL SER ALA SEQRES 2 L 238 ALA VAL GLY GLY THR VAL THR ILE SER CYS GLN SER SER SEQRES 3 L 238 GLN SER VAL TYR ASN ASN ASP ASN LEU ALA TRP TYR GLN SEQRES 4 L 238 GLN LYS PRO GLY GLN PRO PRO LYS ARG LEU ILE TYR GLY SEQRES 5 L 238 ALA SER THR LEU ASP SER GLY VAL PRO SER ARG PHE LYS SEQRES 6 L 238 GLY SER GLY SER GLY THR GLN PHE THR LEU THR ILE SER SEQRES 7 L 238 GLY VAL GLU CYS ASP ASP ALA ALA THR TYR TYR CYS GLN SEQRES 8 L 238 GLY ALA TYR ASN VAL ASP ILE TYR PRO PHE GLY GLY GLY SEQRES 9 L 238 THR GLU VAL VAL VAL LYS GLY ASP PRO VAL ALA PRO THR SEQRES 10 L 238 VAL LEU ILE PHE PRO PRO SER ALA ASP LEU VAL ALA THR SEQRES 11 L 238 GLY THR VAL THR ILE VAL CYS VAL ALA ASN LYS TYR PHE SEQRES 12 L 238 PRO ASP VAL THR VAL THR TRP GLU VAL ASP GLY THR THR SEQRES 13 L 238 GLN THR THR GLY ILE GLU ASN SER LYS THR PRO GLN ASN SEQRES 14 L 238 SER ALA ASP CYS THR TYR ASN LEU SER SER THR LEU THR SEQRES 15 L 238 LEU THR SER THR GLN TYR ASN SER HIS LYS GLU TYR THR SEQRES 16 L 238 CYS LYS VAL THR GLN GLY THR THR SER VAL VAL GLN SER SEQRES 17 L 238 PHE ASN ARG GLY ASP CYS ALA ALA ALA GLU GLN LYS LEU SEQRES 18 L 238 ILE SER GLU GLU ASP LEU ASN SER ALA VAL ASP HIS HIS SEQRES 19 L 238 HIS HIS HIS HIS SEQRES 1 B 14 ASN PRO ILE PHE GLU LYS PHE GLY M3L GLY GLY THR TYR SEQRES 2 B 14 PRO HET M3L B 9 12 HET CL H 301 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM CL CHLORIDE ION FORMUL 3 M3L C9 H21 N2 O2 1+ FORMUL 4 CL CL 1- FORMUL 5 HOH *330(H2 O) HELIX 1 AA1 THR H 83 THR H 87 5 5 HELIX 2 AA2 SER H 157 THR H 159 5 3 HELIX 3 AA3 PRO H 199 ASN H 202 5 4 HELIX 4 AA4 VAL L 29 ASP L 33 5 5 HELIX 5 AA5 GLU L 81 ALA L 85 5 5 HELIX 6 AA6 SER L 124 THR L 130 1 7 HELIX 7 AA7 SER L 185 SER L 190 1 6 HELIX 8 AA8 GLY L 212 CYS L 214 5 3 SHEET 1 AA1 4 SER H 2 SER H 6 0 SHEET 2 AA1 4 LEU H 17 SER H 24 -1 O THR H 22 N GLU H 4 SHEET 3 AA1 4 THR H 74 MET H 79 -1 O ILE H 75 N CYS H 21 SHEET 4 AA1 4 PHE H 66 LYS H 70 -1 N THR H 67 O LYS H 78 SHEET 1 AA2 6 LEU H 10 VAL H 11 0 SHEET 2 AA2 6 THR H 108 VAL H 112 1 O THR H 111 N VAL H 11 SHEET 3 AA2 6 ALA H 88 HIS H 95 -1 N TYR H 90 O THR H 108 SHEET 4 AA2 6 MET H 33 GLN H 38 -1 N GLY H 34 O ALA H 93 SHEET 5 AA2 6 GLU H 45 ILE H 50 -1 O ILE H 47 N TRP H 35 SHEET 6 AA2 6 THR H 56 TYR H 58 -1 O TYR H 57 N ALA H 49 SHEET 1 AA3 4 LEU H 10 VAL H 11 0 SHEET 2 AA3 4 THR H 108 VAL H 112 1 O THR H 111 N VAL H 11 SHEET 3 AA3 4 ALA H 88 HIS H 95 -1 N TYR H 90 O THR H 108 SHEET 4 AA3 4 PHE H 101 TRP H 104 -1 O LEU H 103 N ARG H 94 SHEET 1 AA4 4 SER H 121 LEU H 125 0 SHEET 2 AA4 4 THR H 136 TYR H 146 -1 O LEU H 142 N PHE H 123 SHEET 3 AA4 4 TYR H 177 THR H 186 -1 O LEU H 179 N VAL H 143 SHEET 4 AA4 4 VAL H 164 THR H 166 -1 N ARG H 165 O VAL H 182 SHEET 1 AA5 4 SER H 121 LEU H 125 0 SHEET 2 AA5 4 THR H 136 TYR H 146 -1 O LEU H 142 N PHE H 123 SHEET 3 AA5 4 TYR H 177 THR H 186 -1 O LEU H 179 N VAL H 143 SHEET 4 AA5 4 VAL H 170 ARG H 171 -1 N VAL H 170 O SER H 178 SHEET 1 AA6 3 THR H 152 TRP H 155 0 SHEET 2 AA6 3 VAL H 192 HIS H 198 -1 O ASN H 195 N THR H 154 SHEET 3 AA6 3 THR H 203 VAL H 209 -1 O VAL H 205 N VAL H 196 SHEET 1 AA7 4 MET L 4 THR L 7 0 SHEET 2 AA7 4 THR L 18 SER L 25 -1 O GLN L 24 N THR L 5 SHEET 3 AA7 4 GLN L 72 SER L 78 -1 O ILE L 77 N VAL L 19 SHEET 4 AA7 4 PHE L 64 SER L 69 -1 N LYS L 65 O THR L 76 SHEET 1 AA8 6 SER L 10 ALA L 14 0 SHEET 2 AA8 6 THR L 105 LYS L 110 1 O LYS L 110 N ALA L 13 SHEET 3 AA8 6 ALA L 86 GLY L 92 -1 N ALA L 86 O VAL L 107 SHEET 4 AA8 6 LEU L 35 GLN L 40 -1 N TYR L 38 O TYR L 89 SHEET 5 AA8 6 LYS L 47 TYR L 51 -1 O LEU L 49 N TRP L 37 SHEET 6 AA8 6 THR L 55 LEU L 56 -1 O THR L 55 N TYR L 51 SHEET 1 AA9 4 THR L 117 PHE L 121 0 SHEET 2 AA9 4 THR L 132 TYR L 142 -1 O ASN L 140 N THR L 117 SHEET 3 AA9 4 TYR L 175 THR L 184 -1 O LEU L 181 N ILE L 135 SHEET 4 AA9 4 ILE L 161 LYS L 165 -1 N SER L 164 O SER L 178 SHEET 1 AB1 4 THR L 155 THR L 156 0 SHEET 2 AB1 4 THR L 147 VAL L 152 -1 N VAL L 152 O THR L 155 SHEET 3 AB1 4 GLU L 193 GLN L 200 -1 O LYS L 197 N THR L 149 SHEET 4 AB1 4 THR L 203 ASN L 210 -1 O VAL L 205 N VAL L 198 SSBOND 1 CYS H 21 CYS H 92 1555 1555 2.07 SSBOND 2 CYS H 128 CYS L 214 1555 1555 2.08 SSBOND 3 CYS H 141 CYS H 194 1555 1555 2.06 SSBOND 4 CYS L 23 CYS L 90 1555 1555 2.20 SSBOND 5 CYS L 82 CYS L 173 1555 1555 2.07 SSBOND 6 CYS L 137 CYS L 196 1555 1555 1.97 LINK C GLY B 8 N M3L B 9 1555 1555 1.34 LINK C M3L B 9 N GLY B 10 1555 1555 1.30 CISPEP 1 LEU H 147 PRO H 148 0 -11.64 CISPEP 2 GLU H 149 PRO H 150 0 -5.35 CISPEP 3 THR L 7 PRO L 8 0 -9.25 CISPEP 4 PHE L 143 PRO L 144 0 0.74 SITE 1 AC1 3 THR B 12 SER H 27 ASN H 31 CRYST1 82.329 82.329 120.269 90.00 90.00 90.00 P 41 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 0.012146 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008315 0.00000