HEADER CYTOKINE/DNA 05-NOV-13 4NI7 TITLE CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN 6 IN COMPLEX WITH A MODIFIED TITLE 2 NUCLEOTIDE APTAMER (SOMAMER SL1025) COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-6, B-CELL STIMULATORY FACTOR 2, BSF-2, CTL COMPND 5 DIFFERENTIATION FACTOR, CDF, HYBRIDOMA GROWTH FACTOR, INTERFERON COMPND 6 BETA-2, IFN-BETA-2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SOMAMER SL1025; COMPND 10 CHAIN: B; COMPND 11 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: IL6, IFNB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS INTERLEUKIN-6, CYTOKINE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.DAVIES,T.EDWARDS,A.GELINAS,T.JARVIS,M.C.CLIFTON REVDAT 5 20-SEP-23 4NI7 1 REMARK SEQADV LINK REVDAT 4 01-JUN-16 4NI7 1 AUTHOR REVDAT 3 09-APR-14 4NI7 1 JRNL REVDAT 2 12-FEB-14 4NI7 1 JRNL REVDAT 1 22-JAN-14 4NI7 0 JRNL AUTH A.D.GELINAS,D.R.DAVIES,T.E.EDWARDS,J.C.ROHLOFF,J.D.CARTER, JRNL AUTH 2 C.ZHANG,S.GUPTA,Y.ISHIKAWA,M.HIROTA,Y.NAKAISHI,T.C.JARVIS, JRNL AUTH 3 N.JANJIC JRNL TITL CRYSTAL STRUCTURE OF INTERLEUKIN-6 IN COMPLEX WITH A JRNL TITL 2 MODIFIED NUCLEIC ACID LIGAND. JRNL REF J.BIOL.CHEM. V. 289 8720 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24415767 JRNL DOI 10.1074/JBC.M113.532697 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11384 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 570 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 777 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1130 REMARK 3 NUCLEIC ACID ATOMS : 729 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.15000 REMARK 3 B22 (A**2) : 11.15000 REMARK 3 B33 (A**2) : -22.30000 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): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.151 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.870 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1959 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2779 ; 1.922 ; 2.431 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 148 ; 4.915 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 43 ;45.308 ;24.186 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 195 ;16.021 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;21.769 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 315 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1278 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 753 ; 0.699 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1193 ; 1.286 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1206 ; 1.610 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1586 ; 2.498 ; 4.500 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 16 A 218 REMARK 3 ORIGIN FOR THE GROUP (A): -6.6864 12.1735 8.9461 REMARK 3 T TENSOR REMARK 3 T11: 0.0678 T22: 0.1090 REMARK 3 T33: 0.2194 T12: 0.0185 REMARK 3 T13: 0.0772 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 2.6899 L22: 1.3343 REMARK 3 L33: 4.5929 L12: -0.5615 REMARK 3 L13: -2.1681 L23: 2.0044 REMARK 3 S TENSOR REMARK 3 S11: 0.0703 S12: 0.2612 S13: -0.0575 REMARK 3 S21: 0.1967 S22: -0.1813 S23: 0.1528 REMARK 3 S31: 0.0076 S32: -0.1867 S33: 0.1110 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 : B 1 B 211 REMARK 3 ORIGIN FOR THE GROUP (A): 9.9279 4.5232 6.6574 REMARK 3 T TENSOR REMARK 3 T11: 0.0422 T22: 0.1338 REMARK 3 T33: 0.1777 T12: 0.0329 REMARK 3 T13: 0.0217 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.8952 L22: 2.5957 REMARK 3 L33: 3.1618 L12: 1.5758 REMARK 3 L13: -1.6158 L23: -1.7706 REMARK 3 S TENSOR REMARK 3 S11: -0.1121 S12: 0.0587 S13: -0.1552 REMARK 3 S21: 0.1099 S22: 0.0755 S23: -0.0057 REMARK 3 S31: 0.1480 S32: 0.3598 S33: 0.0365 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 4NI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03318 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11411 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD WITH MR REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1IL6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 31% PEG 3350, 180 MM LINO3, 100 MM REMARK 280 SODIUM ACETATE (PH 5.5), 2.5% HEXAMINE COBALT CHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,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 69.08667 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 34.54333 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 300 REMARK: BIOMOLECULE: NULL 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 300 REMARK 300 REMARK: MONOMER 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 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 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 ALA A 0 REMARK 465 PRO A 1 REMARK 465 VAL A 2 REMARK 465 PRO A 3 REMARK 465 PRO A 4 REMARK 465 GLY A 5 REMARK 465 GLU A 6 REMARK 465 ASP A 7 REMARK 465 SER A 8 REMARK 465 LYS A 9 REMARK 465 ASP A 10 REMARK 465 VAL A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 PRO A 14 REMARK 465 HIS A 15 REMARK 465 ASN A 48 REMARK 465 MET A 49 REMARK 465 CYS A 50 REMARK 465 GLU A 51 REMARK 465 SER A 52 REMARK 465 SER A 53 REMARK 465 LYS A 54 REMARK 465 GLU A 55 REMARK 465 ALA A 56 REMARK 465 LEU A 57 REMARK 465 ALA A 58 REMARK 465 GLU A 59 REMARK 465 ASN A 60 REMARK 465 LYS A 131 REMARK 465 ASN A 132 REMARK 465 LEU A 133 REMARK 465 ASP A 134 REMARK 465 ALA A 135 REMARK 465 OMC B 20 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 GLN A 17 CG CD OE1 NE2 REMARK 470 ARG A 40 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 ASN A 45 CG OD1 ND2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 ASN A 61 CG OD1 ND2 REMARK 470 ASN A 63 CG OD1 ND2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 GLN A 75 CG CD OE1 NE2 REMARK 470 PHE A 78 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 LEU A 84 CG CD1 CD2 REMARK 470 ASN A 103 CG OD1 ND2 REMARK 470 GLU A 106 CG CD OE1 OE2 REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 ILE A 136 CG1 CG2 CD1 REMARK 470 ASP A 140 CG OD1 OD2 REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 ARG A 179 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 183 CG CD OE1 NE2 REMARK 470 MET A 184 CG SD CE REMARK 470 A2M B 19 C5' C4' O4' C3' O3' C2' O2' REMARK 470 A2M B 19 C1' CM' N9 C8 N7 C5 C6 REMARK 470 A2M B 19 N6 N1 C2 N3 C4 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 DUZ B 8 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 UPE B 9 O3' - P - O5' ANGL. DEV. = -16.1 DEGREES REMARK 500 DA B 13 O5' - C5' - C4' ANGL. DEV. = -9.0 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = -8.8 DEGREES REMARK 500 DUZ B 14 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 A2M B 16 O3' - P - OP1 ANGL. DEV. = -34.6 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 A2M B 19 O3' - P - O5' ANGL. DEV. = -44.4 DEGREES REMARK 500 DA B 25 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 26 O4' - C1' - N9 ANGL. DEV. = 4.6 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 THR A 43 -63.24 -92.78 REMARK 500 SER A 108 29.60 -76.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 1 O6 REMARK 620 2 OMG B 6 O6 90.1 REMARK 620 3 UPE B 9 O22 84.1 136.9 REMARK 620 4 DG B 10 O6 125.6 83.7 133.1 REMARK 620 5 DG B 32 O6 78.9 138.7 81.9 71.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 2 O6 REMARK 620 2 DG B 5 O6 87.6 REMARK 620 3 DG B 10 O6 139.5 85.5 REMARK 620 4 DG B 11 O6 141.6 78.6 75.4 REMARK 620 5 DG B 31 O6 88.4 150.4 115.5 86.6 REMARK 620 6 DG B 32 O6 104.2 140.7 61.0 109.1 68.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 102 DBREF 4NI7 A 0 184 UNP P05231 IL6_HUMAN 28 212 DBREF 4NI7 B 1 32 PDB 4NI7 4NI7 1 32 SEQADV 4NI7 MET A -1 UNP P05231 INITIATING METHIONINE SEQRES 1 A 186 MET ALA PRO VAL PRO PRO GLY GLU ASP SER LYS ASP VAL SEQRES 2 A 186 ALA ALA PRO HIS ARG GLN PRO LEU THR SER SER GLU ARG SEQRES 3 A 186 ILE ASP LYS GLN ILE ARG TYR ILE LEU ASP GLY ILE SER SEQRES 4 A 186 ALA LEU ARG LYS GLU THR CYS ASN LYS SER ASN MET CYS SEQRES 5 A 186 GLU SER SER LYS GLU ALA LEU ALA GLU ASN ASN LEU ASN SEQRES 6 A 186 LEU PRO LYS MET ALA GLU LYS ASP GLY CYS PHE GLN SER SEQRES 7 A 186 GLY PHE ASN GLU GLU THR CYS LEU VAL LYS ILE ILE THR SEQRES 8 A 186 GLY LEU LEU GLU PHE GLU VAL TYR LEU GLU TYR LEU GLN SEQRES 9 A 186 ASN ARG PHE GLU SER SER GLU GLU GLN ALA ARG ALA VAL SEQRES 10 A 186 GLN MET SER THR LYS VAL LEU ILE GLN PHE LEU GLN LYS SEQRES 11 A 186 LYS ALA LYS ASN LEU ASP ALA ILE THR THR PRO ASP PRO SEQRES 12 A 186 THR THR ASN ALA SER LEU LEU THR LYS LEU GLN ALA GLN SEQRES 13 A 186 ASN GLN TRP LEU GLN ASP MET THR THR HIS LEU ILE LEU SEQRES 14 A 186 ARG SER PHE LYS GLU PHE LEU GLN SER SER LEU ARG ALA SEQRES 15 A 186 LEU ARG GLN MET SEQRES 1 B 32 DG DG OMC DA DG OMG DUZ DUZ UPE DG DG 2JU DA SEQRES 2 B 32 DUZ DUZ A2M DA DC A2M OMC DG DUZ DUZ DA DA DG SEQRES 3 B 32 DUZ OMC DG DUZ DG DG MODRES 4NI7 OMC B 3 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 4NI7 OMG B 6 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 4NI7 DUZ B 7 DU MODRES 4NI7 DUZ B 8 DU MODRES 4NI7 UPE B 9 DU MODRES 4NI7 DUZ B 14 DU MODRES 4NI7 DUZ B 15 DU MODRES 4NI7 A2M B 16 A MODRES 4NI7 A2M B 19 A MODRES 4NI7 DUZ B 22 DU MODRES 4NI7 DUZ B 23 DU MODRES 4NI7 DUZ B 27 DU MODRES 4NI7 OMC B 28 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 4NI7 DUZ B 30 DU HET OMC B 3 21 HET OMG B 6 24 HET DUZ B 7 29 HET DUZ B 8 29 HET UPE B 9 30 HET 2JU B 12 33 HET DUZ B 14 29 HET DUZ B 15 29 HET A2M B 16 23 HET A2M B 19 4 HET DUZ B 22 29 HET DUZ B 23 29 HET DUZ B 27 29 HET OMC B 28 21 HET DUZ B 30 29 HET NA B 101 1 HET NA B 102 1 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM DUZ 5-(BENZYLCARBAMOYL)-2'-DEOXYURIDINE 5'-(DIHYDROGEN HETNAM 2 DUZ PHOSPHATE) HETNAM UPE 2'-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE 5'- HETNAM 2 UPE (DIHYDROGEN PHOSPHATE) HETNAM 2JU 2'-DEOXY-5-[(NAPHTHALEN-1-YLMETHYL)CARBAMOYL]URIDINE HETNAM 2 2JU 5'-(DIHYDROGEN PHOSPHATE) HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM NA SODIUM ION FORMUL 2 OMC 2(C10 H16 N3 O8 P) FORMUL 2 OMG C11 H16 N5 O8 P FORMUL 2 DUZ 8(C17 H20 N3 O9 P) FORMUL 2 UPE C18 H22 N3 O9 P FORMUL 2 2JU C21 H22 N3 O9 P FORMUL 2 A2M 2(C11 H16 N5 O7 P) FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *29(H2 O) HELIX 1 1 THR A 20 ASN A 45 1 26 HELIX 2 2 ALA A 68 GLY A 72 5 5 HELIX 3 3 ASN A 79 GLN A 102 1 24 HELIX 4 4 SER A 108 ALA A 130 1 23 HELIX 5 5 ASP A 140 GLN A 154 1 15 HELIX 6 6 ASN A 155 ARG A 182 1 28 SSBOND 1 CYS A 73 CYS A 83 1555 1555 2.04 LINK O3' DG B 2 P OMC B 3 1555 1555 1.61 LINK O3' OMC B 3 P DA B 4 1555 1555 1.60 LINK O3' DG B 5 P OMG B 6 1555 1555 1.60 LINK O3' OMG B 6 P DUZ B 7 1555 1555 1.58 LINK O3' DUZ B 7 P DUZ B 8 1555 1555 1.62 LINK O3' DUZ B 8 P UPE B 9 1555 1555 1.61 LINK O3' UPE B 9 P DG B 10 1555 1555 1.61 LINK O3' DG B 11 P 2JU B 12 1555 1555 1.59 LINK O3' 2JU B 12 P DA B 13 1555 1555 1.58 LINK O3' DA B 13 P DUZ B 14 1555 1555 1.58 LINK O3' DUZ B 14 P DUZ B 15 1555 1555 1.61 LINK O3' DUZ B 15 P A2M B 16 1555 1555 1.62 LINK O3' A2M B 16 P DA B 17 1555 1555 1.60 LINK O3' DC B 18 P A2M B 19 1555 1555 1.61 LINK O3' DG B 21 P DUZ B 22 1555 1555 1.60 LINK O3' DUZ B 22 P DUZ B 23 1555 1555 1.60 LINK O3' DUZ B 23 P DA B 24 1555 1555 1.60 LINK O3' DG B 26 P DUZ B 27 1555 1555 1.60 LINK O3' DUZ B 27 P OMC B 28 1555 1555 1.60 LINK O3' OMC B 28 P DG B 29 1555 1555 1.59 LINK O3' DG B 29 P DUZ B 30 1555 1555 1.60 LINK O3' DUZ B 30 P DG B 31 1555 1555 1.60 LINK O6 DG B 1 NA NA B 101 1555 1555 2.45 LINK O6 DG B 2 NA NA B 102 1555 1555 2.24 LINK O6 DG B 5 NA NA B 102 1555 1555 2.41 LINK O6 OMG B 6 NA NA B 101 1555 1555 2.37 LINK O22 UPE B 9 NA NA B 101 1555 1555 2.59 LINK O6 DG B 10 NA NA B 101 1555 1555 2.49 LINK O6 DG B 10 NA NA B 102 1555 1555 2.63 LINK O6 DG B 11 NA NA B 102 1555 1555 2.39 LINK O6 DG B 31 NA NA B 102 1555 1555 2.34 LINK O6 DG B 32 NA NA B 101 1555 1555 2.53 LINK O6 DG B 32 NA NA B 102 1555 1555 3.11 SITE 1 AC1 6 DG B 1 OMG B 6 UPE B 9 DG B 10 SITE 2 AC1 6 DG B 32 NA B 102 SITE 1 AC2 10 DG B 1 DG B 2 DA B 4 DG B 5 SITE 2 AC2 10 OMG B 6 DG B 10 DG B 11 DG B 31 SITE 3 AC2 10 DG B 32 NA B 101 CRYST1 50.230 50.230 103.630 90.00 90.00 120.00 P 32 3 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 0.019908 0.011494 0.000000 0.00000 SCALE2 0.000000 0.022988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009650 0.00000