PDB Short entry for 1TNF HEADER LYMPHOKINE 25-AUG-89 1TNF TITLE THE STRUCTURE OF TUMOR NECROSIS FACTOR-ALPHA AT 2.6 TITLE 2 ANGSTROMS RESOLUTION. IMPLICATIONS FOR RECEPTOR BINDING COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR-ALPHA; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS LYMPHOKINE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.ECK,S.R.SPRANG REVDAT 4 24-FEB-09 1TNF 1 VERSN REVDAT 3 01-APR-03 1TNF 1 JRNL REVDAT 2 15-JAN-91 1TNF 1 REMARK REVDAT 1 15-JAN-90 1TNF 0 JRNL AUTH M.J.ECK,S.R.SPRANG JRNL TITL THE STRUCTURE OF TUMOR NECROSIS FACTOR-ALPHA AT JRNL TITL 2 2.6 A RESOLUTION. IMPLICATIONS FOR RECEPTOR JRNL TITL 3 BINDING. JRNL REF J.BIOL.CHEM. V. 264 17595 1989 JRNL REFN ISSN 0021-9258 JRNL PMID 2551905 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.ECK,B.BEUTLER,G.KUO,J.P.MERRYWEATHER,S.R.SPRANG REMARK 1 TITL CRYSTALLIZATION OF TRIMERIC RECOMBINANT HUMAN REMARK 1 TITL 2 TUMOR NECROSIS FACTOR (CACHECTIN) REMARK 1 REF J.BIOL.CHEM. V. 263 12816 1988 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 4.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TNF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 58.50000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.25000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.75000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.25000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 87.75000 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 58.50000 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: REMARK 300 THE MOLECULE EXISTS AS A TRIMER IN WHICH THE THREE SUBUNITS REMARK 300 ARE RELATED BY APPROXIMATE THREE-FOLD SYMMETRY. THE THREE REMARK 300 SUBUNITS HAVE BEEN ASSIGNED CHAIN INDICATORS A, B, AND C. REMARK 300 THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW REMARK 300 WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED REMARK 300 TO CHAIN A. THE TRANSFORMATION PRESENTED ON *MTRIX 2* REMARK 300 RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN REMARK 300 C WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED ON REMARK 300 *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES REMARK 300 FOR CHAIN C WHEN APPLIED TO CHAIN B. 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: 7040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 VAL A 1 REMARK 465 ARG A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 VAL B 1 REMARK 465 ARG B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 VAL C 1 REMARK 465 ARG C 2 REMARK 465 SER C 3 REMARK 465 SER C 4 REMARK 465 SER C 5 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 A 6 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 6 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 6 CG CD NE CZ NH1 NH2 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 HIS A 15 NE2 HIS A 15 CD2 -0.078 REMARK 500 HIS A 73 NE2 HIS A 73 CD2 -0.067 REMARK 500 HIS A 78 NE2 HIS A 78 CD2 -0.079 REMARK 500 HIS B 15 NE2 HIS B 15 CD2 -0.077 REMARK 500 HIS B 73 NE2 HIS B 73 CD2 -0.067 REMARK 500 HIS B 78 NE2 HIS B 78 CD2 -0.068 REMARK 500 HIS C 15 NE2 HIS C 15 CD2 -0.076 REMARK 500 HIS C 73 NE2 HIS C 73 CD2 -0.071 REMARK 500 HIS C 78 NE2 HIS C 78 CD2 -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 TRP A 28 CD1 - CG - CD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 TRP A 28 CE2 - CD2 - CG ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 32 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 32 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 LEU A 37 N - CA - C ANGL. DEV. = -18.5 DEGREES REMARK 500 LEU A 43 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG A 44 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 44 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 CYS A 69 CA - CB - SG ANGL. DEV. = -15.4 DEGREES REMARK 500 HIS A 73 CA - CB - CG ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 82 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 VAL A 85 CA - CB - CG2 ANGL. DEV. = -11.3 DEGREES REMARK 500 TYR A 87 CA - CB - CG ANGL. DEV. = 13.0 DEGREES REMARK 500 CYS A 101 CA - CB - SG ANGL. DEV. = -11.3 DEGREES REMARK 500 GLN A 102 N - CA - C ANGL. DEV. = -19.0 DEGREES REMARK 500 ARG A 103 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 TRP A 114 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP A 114 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 138 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = 8.1 DEGREES REMARK 500 THR B 7 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 TRP B 28 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP B 28 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 LEU B 29 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 SER B 71 CA - C - N ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG B 82 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 GLN B 88 CA - CB - CG ANGL. DEV. = 22.2 DEGREES REMARK 500 ALA B 111 N - CA - C ANGL. DEV. = 17.0 DEGREES REMARK 500 TRP B 114 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP B 114 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 131 NE - CZ - NH2 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG B 138 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 138 NE - CZ - NH2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TYR B 151 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP C 10 CA - C - N ANGL. DEV. = -14.5 DEGREES REMARK 500 TRP C 28 CD1 - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 TRP C 28 CB - CG - CD1 ANGL. DEV. = -7.8 DEGREES REMARK 500 TRP C 28 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES REMARK 500 TRP C 28 CG - CD2 - CE3 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG C 32 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ALA C 38 CA - C - N ANGL. DEV. = -14.9 DEGREES REMARK 500 ALA C 38 O - C - N ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG C 44 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG C 44 CA - C - N ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG C 82 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 TYR C 87 CA - CB - CG ANGL. DEV. = 11.7 DEGREES REMARK 500 TYR C 87 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 TYR C 87 N - CA - C ANGL. DEV. = -18.8 DEGREES REMARK 500 GLN C 88 CA - CB - CG ANGL. DEV. = -14.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 58 ANGLE DEVIATIONS. 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 SER A 9 154.98 58.28 REMARK 500 ASP A 10 55.79 -90.64 REMARK 500 ALA A 22 98.18 -165.86 REMARK 500 ASN A 30 -133.94 -127.53 REMARK 500 ARG A 31 -33.09 60.04 REMARK 500 ARG A 32 -163.66 -65.01 REMARK 500 ALA A 35 78.59 -116.21 REMARK 500 ALA A 38 -131.11 -116.98 REMARK 500 ASN A 39 77.03 -65.69 REMARK 500 ARG A 44 -107.79 -124.84 REMARK 500 PRO A 70 -126.62 -87.44 REMARK 500 THR A 72 -60.61 31.06 REMARK 500 LEU A 75 103.22 55.43 REMARK 500 SER A 86 -60.69 -123.03 REMARK 500 PRO A 100 -110.81 -68.93 REMARK 500 ARG A 103 172.65 59.19 REMARK 500 GLU A 104 -58.23 143.33 REMARK 500 GLU A 107 -31.40 18.65 REMARK 500 GLU A 110 -87.20 -67.71 REMARK 500 GLN A 149 -73.58 -141.29 REMARK 500 ILE A 155 121.56 -174.04 REMARK 500 PRO B 8 -78.54 -50.97 REMARK 500 SER B 9 146.20 167.72 REMARK 500 ASP B 10 64.27 -103.98 REMARK 500 HIS B 15 77.63 -153.63 REMARK 500 GLN B 21 26.68 -73.04 REMARK 500 ASN B 30 -166.03 -107.29 REMARK 500 ASN B 34 42.98 -148.92 REMARK 500 LEU B 37 96.98 174.36 REMARK 500 ARG B 44 -91.17 -99.22 REMARK 500 ASP B 45 55.54 -93.50 REMARK 500 SER B 60 130.97 -171.65 REMARK 500 THR B 72 -123.74 47.18 REMARK 500 LEU B 75 109.50 52.56 REMARK 500 ALA B 84 -151.23 -49.81 REMARK 500 VAL B 85 -31.99 -140.06 REMARK 500 SER B 86 -102.29 -87.76 REMARK 500 GLN B 88 63.62 -57.32 REMARK 500 ARG B 103 163.73 61.78 REMARK 500 GLU B 104 -50.73 153.78 REMARK 500 PRO B 106 87.78 -67.85 REMARK 500 GLU B 107 -71.30 -56.25 REMARK 500 ALA B 109 -48.37 -148.90 REMARK 500 GLU B 110 -26.84 73.32 REMARK 500 ALA B 111 160.41 73.81 REMARK 500 ALA B 145 45.13 -93.71 REMARK 500 SER B 147 -78.36 -112.27 REMARK 500 GLN B 149 -26.37 -144.57 REMARK 500 PRO C 8 -169.31 -72.71 REMARK 500 SER C 9 75.82 53.10 REMARK 500 PRO C 12 127.54 -37.13 REMARK 500 ALA C 18 -164.34 -76.91 REMARK 500 PRO C 20 38.76 -80.12 REMARK 500 GLU C 23 -40.52 -14.82 REMARK 500 GLN C 25 -56.97 -155.27 REMARK 500 LEU C 26 58.28 88.63 REMARK 500 ARG C 31 -27.14 115.06 REMARK 500 ARG C 32 151.06 -43.68 REMARK 500 ALA C 33 -53.20 -16.54 REMARK 500 ASN C 39 76.83 33.42 REMARK 500 ARG C 44 -113.93 -121.98 REMARK 500 PRO C 51 -147.38 -83.35 REMARK 500 SER C 52 -90.56 36.91 REMARK 500 GLU C 53 158.88 136.41 REMARK 500 THR C 72 150.01 72.41 REMARK 500 LEU C 75 95.80 34.05 REMARK 500 SER C 86 -100.31 -93.20 REMARK 500 GLN C 88 -166.00 -69.95 REMARK 500 THR C 89 165.30 84.36 REMARK 500 GLU C 104 -48.98 -137.67 REMARK 500 PRO C 106 70.52 -20.35 REMARK 500 GLU C 107 -85.93 -90.44 REMARK 500 GLU C 110 128.42 -32.37 REMARK 500 ALA C 111 84.81 20.53 REMARK 500 LYS C 128 110.41 -38.55 REMARK 500 TYR C 141 30.61 -84.03 REMARK 500 ALA C 145 58.55 -172.39 REMARK 500 SER C 147 -78.19 -163.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 7 PRO A 8 117.21 REMARK 500 THR A 105 PRO A 106 -99.71 REMARK 500 THR B 7 PRO B 8 144.02 REMARK 500 THR B 105 PRO B 106 -142.83 REMARK 500 THR C 7 PRO C 8 51.13 REMARK 500 LYS C 11 PRO C 12 135.94 REMARK 500 GLU C 146 SER C 147 141.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 1TNF A 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 1TNF B 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 1TNF C 1 157 UNP P01375 TNFA_HUMAN 77 233 SEQADV 1TNF ASP A 45 UNP P01375 LEU 219 CONFLICT SEQADV 1TNF ASP B 45 UNP P01375 LEU 219 CONFLICT SEQADV 1TNF ASP C 45 UNP P01375 LEU 219 CONFLICT SEQRES 1 A 157 VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO VAL SEQRES 2 A 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU SEQRES 3 A 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN SEQRES 4 A 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER SEQRES 5 A 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE LYS SEQRES 6 A 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS SEQRES 7 A 157 THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS VAL SEQRES 8 A 157 ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU SEQRES 9 A 157 THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO SEQRES 10 A 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY ASP SEQRES 11 A 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU LEU SEQRES 12 A 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 A 157 LEU SEQRES 1 B 157 VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO VAL SEQRES 2 B 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU SEQRES 3 B 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN SEQRES 4 B 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER SEQRES 5 B 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE LYS SEQRES 6 B 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS SEQRES 7 B 157 THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS VAL SEQRES 8 B 157 ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU SEQRES 9 B 157 THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO SEQRES 10 B 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY ASP SEQRES 11 B 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU LEU SEQRES 12 B 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 B 157 LEU SEQRES 1 C 157 VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO VAL SEQRES 2 C 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU SEQRES 3 C 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN SEQRES 4 C 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER SEQRES 5 C 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE LYS SEQRES 6 C 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS SEQRES 7 C 157 THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS VAL SEQRES 8 C 157 ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU SEQRES 9 C 157 THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO SEQRES 10 C 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY ASP SEQRES 11 C 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU LEU SEQRES 12 C 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 C 157 LEU HELIX 1 H1A ARG A 138 LEU A 142 5 5 HELIX 2 H1B ARG B 138 LEU B 142 5 5 HELIX 3 H1C ARG C 138 LEU C 142 5 5 SHEET 1 S1A 5 LEU A 36 ALA A 38 0 SHEET 2 S1A 5 PRO A 12 ALA A 18 -1 N HIS A 15 O LEU A 36 SHEET 3 S1A 5 VAL A 150 LEU A 157 -1 O VAL A 150 N ALA A 18 SHEET 4 S1A 5 GLY A 54 GLY A 68 -1 O GLN A 61 N TYR A 151 SHEET 5 S1A 5 LYS A 112 LEU A 126 -1 N LEU A 126 O GLY A 54 SHEET 1 S2A 5 GLU A 42 ARG A 44 0 SHEET 2 S2A 5 GLN A 47 VAL A 50 -1 O GLN A 47 N ARG A 44 SHEET 3 S2A 5 GLY A 129 ILE A 136 -1 N GLY A 129 O VAL A 50 SHEET 4 S2A 5 LEU A 76 ALA A 84 -1 N THR A 79 O GLU A 135 SHEET 5 S2A 5 GLN A 88 LYS A 98 -1 N VAL A 91 O ARG A 82 SHEET 1 S1B 5 LEU B 36 ALA B 38 0 SHEET 2 S1B 5 PRO B 12 ALA B 18 -1 N HIS B 15 O LEU B 36 SHEET 3 S1B 5 VAL B 150 LEU B 157 -1 O VAL B 150 N ALA B 18 SHEET 4 S1B 5 GLY B 54 GLY B 68 -1 O GLN B 61 N TYR B 151 SHEET 5 S1B 5 LYS B 112 LEU B 126 -1 N LEU B 126 O GLY B 54 SHEET 1 S2B 5 GLU B 42 ARG B 44 0 SHEET 2 S2B 5 GLN B 47 VAL B 50 -1 O GLN B 47 N ARG B 44 SHEET 3 S2B 5 GLY B 129 ILE B 136 -1 N GLY B 129 O VAL B 50 SHEET 4 S2B 5 LEU B 76 ALA B 84 -1 N THR B 79 O GLU B 135 SHEET 5 S2B 5 GLN B 88 LYS B 98 -1 N VAL B 91 O ARG B 82 SHEET 1 S1C 5 LEU C 36 ALA C 38 0 SHEET 2 S1C 5 PRO C 12 ALA C 18 -1 N HIS C 15 O LEU C 36 SHEET 3 S1C 5 VAL C 150 LEU C 157 -1 O VAL C 150 N ALA C 18 SHEET 4 S1C 5 GLY C 54 GLY C 68 -1 O GLN C 61 N TYR C 151 SHEET 5 S1C 5 LYS C 112 LEU C 126 -1 N LEU C 126 O GLY C 54 SHEET 1 S2C 5 GLU C 42 ARG C 44 0 SHEET 2 S2C 5 GLN C 47 VAL C 50 -1 O GLN C 47 N ARG C 44 SHEET 3 S2C 5 GLY C 129 ILE C 136 -1 N GLY C 129 O VAL C 50 SHEET 4 S2C 5 LEU C 76 ALA C 84 -1 N THR C 79 O GLU C 135 SHEET 5 S2C 5 GLN C 88 LYS C 98 -1 N VAL C 91 O ARG C 82 SSBOND 1 CYS A 69 CYS A 101 1555 1555 1.99 SSBOND 2 CYS B 69 CYS B 101 1555 1555 2.03 SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.02 CRYST1 95.000 95.000 117.000 90.00 90.00 90.00 P 41 21 2 24 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 0.010526 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008547 0.00000 MTRIX1 1 0.040460 -0.105750 0.993570 -16.17000 1 MTRIX2 1 -0.980650 0.186430 0.059780 57.43000 1 MTRIX3 1 -0.191550 -0.976760 -0.096160 96.33000 1 MTRIX1 2 -0.028960 -0.992710 -0.116990 74.40000 1 MTRIX2 2 -0.202020 0.120440 -0.971950 87.33000 1 MTRIX3 2 0.978950 -0.004510 -0.204040 28.89000 1 MTRIX1 3 -0.012020 -0.163460 0.986460 -11.46000 1 MTRIX2 3 -0.986560 0.162730 0.014940 60.62000 1 MTRIX3 3 -0.162970 -0.973040 -0.163220 97.89000 1