HEADER CYTOKINE/INHIBITOR 01-JUL-14 4TWT TITLE HUMAN TNFA DIMER IN COMPLEX WITH THE SEMI-SYNTHETIC BICYCLIC PEPTIDE TITLE 2 M21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 77-233; COMPND 5 SYNONYM: CACHECTIN,TNF-ALPHA,TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY COMPND 6 MEMBER 2,TNF-A; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ALA-CYS-PRO-PRO-CYS-LEU-TRP-GLN-VAL-LEU-CYS-GLY; COMPND 10 CHAIN: E, F; COMPND 11 SYNONYM: PEPTIDE M21; COMPND 12 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: TNF, TNFA, TNFSF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS TUMOR NECROSIS FACTOR-ALPHA, BICYCLO COMPOUNDS, PEPTIDES, CYTOKINE- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.LUZI,Y.KONDO,E.BERNARD,L.STADLER,G.WINTER,P.HOLLIGER REVDAT 2 20-DEC-23 4TWT 1 REMARK REVDAT 1 04-FEB-15 4TWT 0 JRNL AUTH S.LUZI,Y.KONDO,E.BERNARD,L.K.STADLER,M.VAYSBURD,G.WINTER, JRNL AUTH 2 P.HOLLIGER JRNL TITL SUBUNIT DISASSEMBLY AND INHIBITION OF TNF ALPHA BY A JRNL TITL 2 SEMI-SYNTHETIC BICYCLIC PEPTIDE. JRNL REF PROTEIN ENG.DES.SEL. V. 28 45 2015 JRNL REFN ESSN 1741-0134 JRNL PMID 25614525 JRNL DOI 10.1093/PROTEIN/GZU055 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18737 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1005 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) : 2.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1360 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3710 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.4420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4533 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : 0.31000 REMARK 3 B33 (A**2) : -1.00000 REMARK 3 B12 (A**2) : 0.15000 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): 3.012 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.414 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.355 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.940 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4696 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4509 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6383 ; 1.692 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10315 ; 2.596 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 574 ; 6.892 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;39.507 ;24.550 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 726 ;17.151 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.942 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 725 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5283 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1057 ; 0.006 ; 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): 2331 ; 5.801 ; 8.172 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2331 ; 5.801 ; 8.172 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2892 ; 9.173 ;12.219 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2893 ; 9.171 ;12.220 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2365 ; 5.701 ; 8.442 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2365 ; 5.693 ; 8.443 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3492 ; 8.722 ;12.521 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 18211 ;14.881 ;76.393 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 18210 ;14.881 ;76.394 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 7 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 10 157 B 10 157 7253 0.16 0.05 REMARK 3 2 A 9 157 C 9 157 7540 0.16 0.05 REMARK 3 3 A 9 157 D 9 157 6567 0.18 0.05 REMARK 3 4 B 10 157 C 10 157 7042 0.17 0.05 REMARK 3 5 B 10 157 D 10 157 6791 0.16 0.05 REMARK 3 6 E 1 12 F 1 12 476 0.12 0.05 REMARK 3 7 C 9 157 D 9 157 6621 0.18 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4TWT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19797 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 46.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 1.24700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 1TNF REMARK 200 REMARK 200 REMARK: HEXAGONAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25.5% PEG 8000, 0.085 M NA CACODYLATE REMARK 280 PH 6.5, 0.17M AMMONIUM SULFATE, 15% GLYCEROL., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 153.58333 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 76.79167 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 76.79167 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 153.58333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, C, D 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 ARG A 6 REMARK 465 THR A 7 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 ARG B 6 REMARK 465 THR B 7 REMARK 465 PRO B 8 REMARK 465 SER B 9 REMARK 465 ARG B 32 REMARK 465 ALA B 33 REMARK 465 ASN B 34 REMARK 465 ALA B 35 REMARK 465 PRO B 106 REMARK 465 GLU B 107 REMARK 465 GLY B 108 REMARK 465 ALA B 109 REMARK 465 GLU B 110 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 465 ARG C 6 REMARK 465 THR C 7 REMARK 465 PRO C 8 REMARK 465 PRO C 106 REMARK 465 GLU C 107 REMARK 465 GLY C 108 REMARK 465 ALA C 109 REMARK 465 GLU C 110 REMARK 465 ALA C 111 REMARK 465 VAL D 1 REMARK 465 ARG D 2 REMARK 465 SER D 3 REMARK 465 SER D 4 REMARK 465 SER D 5 REMARK 465 ARG D 6 REMARK 465 THR D 7 REMARK 465 PRO D 8 REMARK 465 ARG D 32 REMARK 465 ALA D 33 REMARK 465 ASN D 34 REMARK 465 ALA D 35 REMARK 465 LEU D 36 REMARK 465 LEU D 37 REMARK 465 ALA D 38 REMARK 465 PRO D 70 REMARK 465 GLU D 104 REMARK 465 THR D 105 REMARK 465 PRO D 106 REMARK 465 GLU D 107 REMARK 465 GLY D 108 REMARK 465 ALA D 109 REMARK 465 GLU D 110 REMARK 465 ALA D 111 REMARK 465 LYS D 112 REMARK 465 ASP D 143 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 21 CG CD OE1 NE2 REMARK 470 GLU A 23 CG CD OE1 OE2 REMARK 470 ARG A 32 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 LEU A 157 O REMARK 470 ARG B 103 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 104 CG CD OE1 OE2 REMARK 470 LYS B 112 CG CD CE NZ REMARK 470 LEU B 157 O REMARK 470 GLU C 23 CG CD OE1 OE2 REMARK 470 ARG C 103 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 104 CG CD OE1 OE2 REMARK 470 LYS C 112 CG CD CE NZ REMARK 470 LEU C 157 O REMARK 470 GLU D 23 CG CD OE1 OE2 REMARK 470 ARG D 31 CG CD NE CZ NH1 NH2 REMARK 470 HIS D 73 CG ND1 CD2 CE1 NE2 REMARK 470 LEU D 157 O 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 O ALA C 38 O HOH C 308 1.92 REMARK 500 O GLU A 107 O ALA A 109 2.09 REMARK 500 O VAL C 13 O LEU C 37 2.13 REMARK 500 OXT GLY E 12 O2 GOL E 102 2.14 REMARK 500 O CYS C 69 O GLU C 104 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 B 39 35.39 73.62 REMARK 500 ALA C 38 31.23 71.37 REMARK 500 ASN C 39 -61.96 73.51 REMARK 500 HIS C 73 52.88 -90.84 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 ARG A 31 ARG A 32 143.50 REMARK 500 SER D 86 TYR D 87 -125.96 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 GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for peptide chain E REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for peptide chain F DBREF 4TWT A 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 4TWT B 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 4TWT E 1 12 PDB 4TWT 4TWT 1 12 DBREF 4TWT F 1 12 PDB 4TWT 4TWT 1 12 DBREF 4TWT C 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 4TWT D 1 157 UNP P01375 TNFA_HUMAN 77 233 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 ASP 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 ASP SEQRES 12 B 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 B 157 LEU SEQRES 1 E 12 ALA CYS PRO PRO CYS LEU TRP GLN VAL LEU CYS GLY SEQRES 1 F 12 ALA CYS PRO PRO CYS LEU TRP GLN VAL LEU CYS GLY 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 ASP SEQRES 12 C 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 C 157 LEU SEQRES 1 D 157 VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO VAL SEQRES 2 D 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU SEQRES 3 D 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN SEQRES 4 D 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER SEQRES 5 D 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE LYS SEQRES 6 D 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS SEQRES 7 D 157 THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS VAL SEQRES 8 D 157 ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU SEQRES 9 D 157 THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO SEQRES 10 D 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY ASP SEQRES 11 D 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP SEQRES 12 D 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA SEQRES 13 D 157 LEU HET GOL B 201 6 HET GOL B 202 6 HET GOL E 101 6 HET GOL E 102 6 HET 38A E 103 12 HET 38A F 101 12 HET GOL C 201 6 HET GOL D 201 6 HETNAM GOL GLYCEROL HETNAM 38A (2,4,6-TRIMETHYLBENZENE-1,3,5-TRIYL)TRIMETHANOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 7 GOL 6(C3 H8 O3) FORMUL 11 38A 2(C12 H18 O3) FORMUL 15 HOH *36(H2 O) HELIX 1 AA1 ARG A 138 LEU A 142 5 5 HELIX 2 AA2 ARG B 138 LEU B 142 5 5 HELIX 3 AA3 TRP E 7 GLY E 12 5 6 HELIX 4 AA4 CYS F 5 CYS F 11 5 7 HELIX 5 AA5 ARG C 138 LEU C 142 5 5 HELIX 6 AA6 ARG D 138 LEU D 142 5 5 SHEET 1 AA1 3 TRP A 28 LEU A 29 0 SHEET 2 AA1 3 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 AA1 3 LEU A 36 ALA A 38 -1 O LEU A 36 N HIS A 15 SHEET 1 AA2 5 TRP A 28 LEU A 29 0 SHEET 2 AA2 5 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 AA2 5 TYR A 151 ALA A 156 -1 O PHE A 152 N VAL A 16 SHEET 4 AA2 5 GLY A 54 GLN A 67 -1 N TYR A 59 O GLY A 153 SHEET 5 AA2 5 PRO A 113 LEU A 126 -1 O TRP A 114 N GLY A 66 SHEET 1 AA310 GLU A 42 ARG A 44 0 SHEET 2 AA310 GLN A 47 VAL A 49 -1 O VAL A 49 N GLU A 42 SHEET 3 AA310 ARG A 131 ILE A 136 -1 O LEU A 132 N LEU A 48 SHEET 4 AA310 LEU A 76 ILE A 83 -1 N THR A 79 O GLU A 135 SHEET 5 AA310 LYS A 90 LYS A 98 -1 O LYS A 98 N LEU A 76 SHEET 6 AA310 LYS C 90 LYS C 98 -1 O LYS C 90 N SER A 95 SHEET 7 AA310 LEU C 76 ILE C 83 -1 N LEU C 76 O LYS C 98 SHEET 8 AA310 ARG C 131 ILE C 136 -1 O GLU C 135 N THR C 79 SHEET 9 AA310 GLN C 47 VAL C 49 -1 N LEU C 48 O LEU C 132 SHEET 10 AA310 GLU C 42 ARG C 44 -1 N GLU C 42 O VAL C 49 SHEET 1 AA4 4 VAL B 13 VAL B 17 0 SHEET 2 AA4 4 TYR B 151 ALA B 156 -1 O PHE B 152 N VAL B 16 SHEET 3 AA4 4 GLY B 54 GLN B 67 -1 N TYR B 59 O GLY B 153 SHEET 4 AA4 4 PRO B 113 LEU B 126 -1 O TRP B 114 N GLY B 66 SHEET 1 AA5 5 GLU B 42 ARG B 44 0 SHEET 2 AA5 5 GLN B 47 VAL B 49 -1 O VAL B 49 N GLU B 42 SHEET 3 AA5 5 ARG B 131 ILE B 136 -1 O LEU B 132 N LEU B 48 SHEET 4 AA5 5 LEU B 76 ILE B 83 -1 N THR B 79 O GLU B 135 SHEET 5 AA5 5 LYS B 90 LYS B 98 -1 O LYS B 98 N LEU B 76 SHEET 1 AA6 5 TRP C 28 LEU C 29 0 SHEET 2 AA6 5 VAL C 13 ALA C 18 -1 N VAL C 17 O LEU C 29 SHEET 3 AA6 5 TYR C 151 ALA C 156 -1 O PHE C 152 N VAL C 16 SHEET 4 AA6 5 GLY C 54 GLN C 67 -1 N TYR C 59 O GLY C 153 SHEET 5 AA6 5 PRO C 113 LEU C 126 -1 O TRP C 114 N GLY C 66 SHEET 1 AA7 5 TRP D 28 LEU D 29 0 SHEET 2 AA7 5 VAL D 13 ALA D 18 -1 N VAL D 17 O LEU D 29 SHEET 3 AA7 5 TYR D 151 ALA D 156 -1 O PHE D 152 N VAL D 16 SHEET 4 AA7 5 GLY D 54 GLY D 66 -1 N TYR D 59 O GLY D 153 SHEET 5 AA7 5 TRP D 114 LEU D 126 -1 O TRP D 114 N GLY D 66 SHEET 1 AA8 5 GLU D 42 ARG D 44 0 SHEET 2 AA8 5 GLN D 47 VAL D 49 -1 O VAL D 49 N GLU D 42 SHEET 3 AA8 5 ARG D 131 ILE D 136 -1 O LEU D 132 N LEU D 48 SHEET 4 AA8 5 LEU D 76 ILE D 83 -1 N THR D 79 O GLU D 135 SHEET 5 AA8 5 LYS D 90 LYS D 98 -1 O LYS D 98 N LEU D 76 SSBOND 1 CYS A 69 CYS A 101 1555 1555 1.95 SSBOND 2 CYS B 69 CYS B 101 1555 1555 1.99 SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.01 SSBOND 4 CYS D 69 CYS D 101 1555 1555 2.02 LINK SG CYS E 2 CAK 38A E 103 1555 1555 1.66 LINK SG CYS E 5 CAJ 38A E 103 1555 1555 1.68 LINK SG CYS E 11 CAL 38A E 103 1555 1555 1.66 LINK SG CYS F 2 CAK 38A F 101 1555 1555 1.60 LINK SG CYS F 5 CAJ 38A F 101 1555 1555 1.65 LINK SG CYS F 11 CAL 38A F 101 1555 1555 1.63 SITE 1 AC1 4 TYR A 119 PRO B 117 ILE B 118 TYR B 119 SITE 1 AC2 5 LEU B 26 ALA B 134 GLU B 135 ILE B 136 SITE 2 AC2 5 PRO B 139 SITE 1 AC3 4 ARG A 138 TYR A 141 ALA E 1 CYS E 2 SITE 1 AC4 1 GLY E 12 SITE 1 AC5 1 PRO C 51 SITE 1 AC6 4 PRO C 117 ILE C 118 TYR C 119 TYR D 119 SITE 1 AC7 13 LEU A 57 TYR A 119 ARG A 138 TYR A 141 SITE 2 AC7 13 LEU A 157 HIS B 15 LEU B 57 TYR B 59 SITE 3 AC7 13 LEU B 120 GLY B 148 GLN B 149 TYR B 151 SITE 4 AC7 13 TYR C 87 SITE 1 AC8 9 TYR C 119 LEU C 157 HIS D 15 LEU D 57 SITE 2 AC8 9 TYR D 59 SER D 147 GLY D 148 GLN D 149 SITE 3 AC8 9 TYR D 151 CRYST1 78.444 78.444 230.375 90.00 90.00 120.00 P 32 2 1 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 0.012748 0.007360 0.000000 0.00000 SCALE2 0.000000 0.014720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004341 0.00000