HEADER IMMUNE SYSTEM 02-MAR-17 5NBI TITLE PRINCIPLES FOR COMPUTATIONAL DESIGN OF ANTIBODIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGN OF ANTIBODIES; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DESIGN OF ANTIBODIES; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTIBODIES, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR O.DYM,S.J.FLEISHMAN REVDAT 6 17-JAN-24 5NBI 1 REMARK REVDAT 5 20-FEB-19 5NBI 1 REMARK LINK REVDAT 4 12-SEP-18 5NBI 1 SOURCE REVDAT 3 08-NOV-17 5NBI 1 JRNL REVDAT 2 18-OCT-17 5NBI 1 JRNL REVDAT 1 27-SEP-17 5NBI 0 JRNL AUTH D.BARAN,M.G.PSZOLLA,G.D.LAPIDOTH,C.NORN,O.DYM,T.UNGER, JRNL AUTH 2 S.ALBECK,M.D.TYKA,S.J.FLEISHMAN JRNL TITL PRINCIPLES FOR COMPUTATIONAL DESIGN OF BINDING ANTIBODIES. JRNL REF PROC. NATL. ACAD. SCI. V. 114 10900 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28973872 JRNL DOI 10.1073/PNAS.1707171114 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 27279 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1405 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1959 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3303 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.46000 REMARK 3 B22 (A**2) : 0.46000 REMARK 3 B33 (A**2) : -1.48000 REMARK 3 B12 (A**2) : 0.23000 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): 0.228 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.168 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.506 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3392 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2977 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4616 ; 1.450 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6962 ; 0.909 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 7.239 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;37.132 ;24.307 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 524 ;13.997 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;21.315 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 509 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3773 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 676 ; 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): 1733 ; 2.603 ; 3.054 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1732 ; 2.600 ; 3.053 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2161 ; 3.842 ; 4.568 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2162 ; 3.841 ; 4.568 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1658 ; 2.970 ; 3.373 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1659 ; 2.969 ; 3.374 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2456 ; 4.571 ; 4.914 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3440 ; 6.405 ;34.861 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3441 ; 6.404 ;34.869 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 : H 3 H 221 REMARK 3 ORIGIN FOR THE GROUP (A): 62.1090 21.6300 202.9370 REMARK 3 T TENSOR REMARK 3 T11: 0.0247 T22: 0.0669 REMARK 3 T33: 0.1563 T12: -0.0030 REMARK 3 T13: 0.0369 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 2.8632 L22: 0.9379 REMARK 3 L33: 2.9828 L12: -0.3107 REMARK 3 L13: 0.1803 L23: -0.6901 REMARK 3 S TENSOR REMARK 3 S11: -0.0755 S12: -0.2353 S13: -0.0079 REMARK 3 S21: -0.0545 S22: 0.0548 S23: 0.0138 REMARK 3 S31: -0.0122 S32: -0.2538 S33: 0.0208 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 216 REMARK 3 ORIGIN FOR THE GROUP (A): 73.4480 28.7130 190.5040 REMARK 3 T TENSOR REMARK 3 T11: 0.1441 T22: 0.0504 REMARK 3 T33: 0.2121 T12: -0.0728 REMARK 3 T13: 0.0202 T23: 0.0237 REMARK 3 L TENSOR REMARK 3 L11: 2.9306 L22: 0.2860 REMARK 3 L33: 1.6589 L12: -0.8853 REMARK 3 L13: 0.3254 L23: -0.1094 REMARK 3 S TENSOR REMARK 3 S11: -0.1246 S12: -0.0705 S13: -0.0159 REMARK 3 S21: -0.0053 S22: 0.0533 S23: 0.0156 REMARK 3 S31: -0.1707 S32: 0.0446 S33: 0.0713 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5NBI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003840. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97242 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28196 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 60.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 3QQ9, 4JFZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NH4CH3CO2 0.05M MG(CH3CO2)2 0.05M REMARK 280 CACODYLATE PH=6.5 15% PEG 8000, PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.72700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 121.45400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 121.45400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.72700 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: 3550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 GLN H 1 REMARK 465 VAL H 2 REMARK 465 THR H 139 REMARK 465 LYS H 222 REMARK 465 SER H 223 REMARK 465 CYS H 224 REMARK 465 ASP H 225 REMARK 465 LYS H 226 REMARK 465 THR H 227 REMARK 465 HIS H 228 REMARK 465 THR H 229 REMARK 465 CYS H 230 REMARK 465 PRO H 231 REMARK 465 PRO H 232 REMARK 465 CYS H 233 REMARK 465 GLU L 217 REMARK 465 CYS L 218 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS H 137 CG CD CE NZ 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 CE2 TRP H 33 CD ARG H 52 1.45 REMARK 500 NE1 TRP H 33 CD ARG H 52 1.53 REMARK 500 CD1 TRP H 33 CG ARG H 52 1.59 REMARK 500 NE1 TRP H 33 CG ARG H 52 1.94 REMARK 500 CE2 TRP H 33 NE ARG H 52 1.94 REMARK 500 CG TRP H 33 CG ARG H 52 1.99 REMARK 500 CZ2 TRP H 33 NE ARG H 52 2.11 REMARK 500 O ASN H 53 N SER H 55 2.17 REMARK 500 CD2 TRP H 33 CD ARG H 52 2.19 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 ASN H 53 -65.20 -170.13 REMARK 500 LYS H 54 -60.04 49.01 REMARK 500 SER H 55 -34.65 -131.19 REMARK 500 TYR H 104 -72.15 -66.72 REMARK 500 LYS H 137 153.57 71.00 REMARK 500 ALA L 55 -48.19 72.64 REMARK 500 ASN L 156 -5.23 72.53 REMARK 500 ARG L 215 95.80 -47.87 REMARK 500 REMARK 500 REMARK: NULL DBREF 5NBI H 1 233 PDB 5NBI 5NBI 1 233 DBREF 5NBI L 1 218 PDB 5NBI 5NBI 1 218 SEQRES 1 H 233 GLN VAL GLN LEU GLN GLU THR GLY GLY GLY LEU VAL GLN SEQRES 2 H 233 PRO GLY GLY SER MET LYS ILE SER CYS VAL THR SER GLY SEQRES 3 H 233 PHE ASN PHE SER HIS ALA TRP MET SER TRP VAL ARG GLN SEQRES 4 H 233 SER PRO GLY LYS GLY LEU GLU TRP VAL ALA GLU ILE ARG SEQRES 5 H 233 ASN LYS SER ASP GLY TYR THR THR TYR TYR ALA PRO SER SEQRES 6 H 233 VAL LYS GLY ARG PHE THR VAL SER ARG ASP ASP SER GLN SEQRES 7 H 233 ASN MET VAL TYR LEU GLN MET ASN ASN LEU ARG ALA GLU SEQRES 8 H 233 ASP THR GLY ILE TYR TYR CYS ALA GLN SER SER PRO TYR SEQRES 9 H 233 SER ARG ALA MET ASP TYR TRP GLY GLN GLY THR THR VAL SEQRES 10 H 233 THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE SEQRES 11 H 233 PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR SEQRES 12 H 233 ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU SEQRES 13 H 233 PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER SEQRES 14 H 233 GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY SEQRES 15 H 233 LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SEQRES 16 H 233 SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS SEQRES 17 H 233 LYS PRO SER ASN THR LYS VAL ASP LYS ARG VAL GLU PRO SEQRES 18 H 233 LYS SER CYS ASP LYS THR HIS THR CYS PRO PRO CYS SEQRES 1 L 218 ASP ILE VAL LEU THR GLN THR PRO LEU THR LEU PRO VAL SEQRES 2 L 218 SER PRO GLY GLN ARG ALA THR ILE SER CYS ARG ALA SER SEQRES 3 L 218 GLN SER VAL ASP ASP ASN GLY HIS SER PHE MET ASN TRP SEQRES 4 L 218 TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU LEU VAL SEQRES 5 L 218 HIS ALA ALA SER TYR VAL LYS SER GLY VAL PRO ALA ARG SEQRES 6 L 218 PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU THR SEQRES 7 L 218 ILE HIS PRO VAL GLU PRO GLU ASP PHE ALA THR TYR TYR SEQRES 8 L 218 CYS GLN GLN GLY TYR SER HIS PRO TRP THR PHE GLY GLY SEQRES 9 L 218 GLY THR LYS LEU GLU ILE LYS ARG THR VAL ALA ALA PRO SEQRES 10 L 218 SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SEQRES 11 L 218 SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE SEQRES 12 L 218 TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN SEQRES 13 L 218 ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU SEQRES 14 L 218 GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER THR SEQRES 15 L 218 LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL SEQRES 16 L 218 TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO SEQRES 17 L 218 VAL THR LYS SER PHE ASN ARG GLY GLU CYS FORMUL 3 HOH *8(H2 O) HELIX 1 AA1 ASP H 76 GLN H 78 5 3 HELIX 2 AA2 ARG H 89 THR H 93 5 5 HELIX 3 AA3 SER H 164 ALA H 166 5 3 HELIX 4 AA4 SER H 195 LEU H 197 5 3 HELIX 5 AA5 GLU L 83 PHE L 87 5 5 HELIX 6 AA6 SER L 125 SER L 131 1 7 HELIX 7 AA7 LYS L 187 LYS L 192 1 6 SHEET 1 AA1 4 LEU H 4 THR H 7 0 SHEET 2 AA1 4 MET H 18 THR H 24 -1 O SER H 21 N THR H 7 SHEET 3 AA1 4 MET H 80 MET H 85 -1 O LEU H 83 N ILE H 20 SHEET 4 AA1 4 PHE H 70 ASP H 75 -1 N SER H 73 O TYR H 82 SHEET 1 AA2 6 LEU H 11 VAL H 12 0 SHEET 2 AA2 6 THR H 115 VAL H 119 1 O THR H 118 N VAL H 12 SHEET 3 AA2 6 GLY H 94 SER H 101 -1 N TYR H 96 O THR H 115 SHEET 4 AA2 6 TRP H 33 SER H 40 -1 N SER H 35 O ALA H 99 SHEET 5 AA2 6 GLY H 44 ILE H 51 -1 O ILE H 51 N MET H 34 SHEET 6 AA2 6 THR H 60 TYR H 62 -1 O TYR H 61 N GLU H 50 SHEET 1 AA3 4 SER H 128 LEU H 132 0 SHEET 2 AA3 4 THR H 143 TYR H 153 -1 O LYS H 151 N SER H 128 SHEET 3 AA3 4 TYR H 184 PRO H 193 -1 O TYR H 184 N TYR H 153 SHEET 4 AA3 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 189 SHEET 1 AA4 4 SER H 128 LEU H 132 0 SHEET 2 AA4 4 THR H 143 TYR H 153 -1 O LYS H 151 N SER H 128 SHEET 3 AA4 4 TYR H 184 PRO H 193 -1 O TYR H 184 N TYR H 153 SHEET 4 AA4 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 185 SHEET 1 AA5 3 THR H 159 TRP H 162 0 SHEET 2 AA5 3 ILE H 203 HIS H 208 -1 O ASN H 207 N THR H 159 SHEET 3 AA5 3 THR H 213 ARG H 218 -1 O THR H 213 N HIS H 208 SHEET 1 AA6 4 LEU L 4 THR L 7 0 SHEET 2 AA6 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA6 4 ASP L 74 ILE L 79 -1 O LEU L 77 N ILE L 21 SHEET 4 AA6 4 PHE L 66 SER L 71 -1 N SER L 69 O THR L 76 SHEET 1 AA7 6 THR L 10 VAL L 13 0 SHEET 2 AA7 6 THR L 106 ILE L 110 1 O GLU L 109 N VAL L 13 SHEET 3 AA7 6 THR L 89 GLN L 94 -1 N TYR L 90 O THR L 106 SHEET 4 AA7 6 MET L 37 GLN L 42 -1 N ASN L 38 O GLN L 93 SHEET 5 AA7 6 LYS L 49 HIS L 53 -1 O LEU L 51 N TRP L 39 SHEET 6 AA7 6 TYR L 57 VAL L 58 -1 O TYR L 57 N HIS L 53 SHEET 1 AA8 4 THR L 10 VAL L 13 0 SHEET 2 AA8 4 THR L 106 ILE L 110 1 O GLU L 109 N VAL L 13 SHEET 3 AA8 4 THR L 89 GLN L 94 -1 N TYR L 90 O THR L 106 SHEET 4 AA8 4 THR L 101 PHE L 102 -1 O THR L 101 N GLN L 94 SHEET 1 AA9 2 ASP L 30 ASP L 31 0 SHEET 2 AA9 2 HIS L 34 SER L 35 -1 O HIS L 34 N ASP L 31 SHEET 1 AB1 4 SER L 118 PHE L 122 0 SHEET 2 AB1 4 THR L 133 PHE L 143 -1 O LEU L 139 N PHE L 120 SHEET 3 AB1 4 TYR L 177 SER L 186 -1 O TYR L 177 N PHE L 143 SHEET 4 AB1 4 SER L 163 VAL L 167 -1 N SER L 166 O SER L 180 SHEET 1 AB2 4 ALA L 157 LEU L 158 0 SHEET 2 AB2 4 LYS L 149 VAL L 154 -1 N VAL L 154 O ALA L 157 SHEET 3 AB2 4 VAL L 195 THR L 201 -1 O GLU L 199 N GLN L 151 SHEET 4 AB2 4 VAL L 209 ASN L 214 -1 O VAL L 209 N VAL L 200 SSBOND 1 CYS H 22 CYS H 98 1555 1555 2.04 SSBOND 2 CYS H 148 CYS H 204 1555 1555 2.07 SSBOND 3 CYS L 23 CYS L 92 1555 1555 2.10 SSBOND 4 CYS L 138 CYS L 198 1555 1555 2.00 CISPEP 1 PHE H 154 PRO H 155 0 -8.58 CISPEP 2 GLU H 156 PRO H 157 0 1.61 CISPEP 3 THR L 7 PRO L 8 0 4.27 CISPEP 4 HIS L 80 PRO L 81 0 -0.84 CISPEP 5 HIS L 98 PRO L 99 0 -5.75 CISPEP 6 TYR L 144 PRO L 145 0 3.48 CRYST1 67.909 67.909 182.181 90.00 90.00 120.00 P 31 2 1 6 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 0.014726 0.008502 0.000000 0.00000 SCALE2 0.000000 0.017004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005489 0.00000