PDB Short entry for 3L9J HEADER IMMUNE SYSTEM 05-JAN-10 3L9J TITLE SELECTION OF A NOVEL HIGHLY SPECIFIC TNFALPHA ANTAGONIST: INSIGHT FROM TITLE 2 THE CRYSTAL STRUCTURE OF THE ANTAGONIST-TNFALPHA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNFALPHA; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TUMOR NECROSIS FACTOR, SOLUBLE FORM; COMPND 7 CHAIN: T; COMPND 8 FRAGMENT: UNP RESIDUES 85-233; COMPND 9 SYNONYM: TNF-ALPHA, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER COMPND 10 2, TNF-A, CACHECTIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7CIIH6; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PT7CIIH6 KEYWDS TNF-ALPHA, ANTAGONIST, IN VITRO SELECTION, CELL MEMBRANE, CYTOKINE, KEYWDS 2 DISULFIDE BOND, GLYCOPROTEIN, LIPOPROTEIN, SECRETED, SIGNAL-ANCHOR, KEYWDS 3 TRANSMEMBRANE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.BYLA,M.H.ANDERSEN,H.C.THOGERSEN,H.H.GAD,R.HARTMANN REVDAT 5 01-NOV-23 3L9J 1 REMARK DBREF LINK REVDAT 4 31-JAN-18 3L9J 1 REMARK REVDAT 3 26-FEB-14 3L9J 1 REMARK VERSN REVDAT 2 21-APR-10 3L9J 1 JRNL REVDAT 1 23-FEB-10 3L9J 0 JRNL AUTH P.BYLA,M.H.ANDERSEN,T.L.HOLTET,H.JACOBSEN,M.MUNCH,H.H.GAD, JRNL AUTH 2 H.C.THOGERSEN,R.HARTMANN JRNL TITL SELECTION OF A NOVEL AND HIGHLY SPECIFIC TNF{ALPHA} JRNL TITL 2 ANTAGONIST: INSIGHT FROM THE CRYSTAL STRUCTURE OF THE JRNL TITL 3 ANTAGONIST-TNF{ALPHA} COMPLEX JRNL REF J.BIOL.CHEM. V. 285 12096 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20179326 JRNL DOI 10.1074/JBC.M109.063305 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17855 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 968 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) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1261 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2206 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29000 REMARK 3 B22 (A**2) : 0.29000 REMARK 3 B33 (A**2) : -0.44000 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): 0.205 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.172 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.821 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2267 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3082 ; 1.475 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 6.420 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;38.431 ;24.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 365 ;13.126 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.222 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 328 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1756 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 928 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1543 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 203 ; 0.191 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.045 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 62 ; 0.234 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.319 ; 0.200 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): 1417 ; 1.129 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2224 ; 1.977 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 987 ; 2.915 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 858 ; 4.718 ; 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 : 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 3L9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG; MAX II REMARK 200 BEAMLINE : X12; I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81500; 1.0 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17855 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 74.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1TNF FOR CHAIN T AND 1TN3 FOR CHAIN C; REMARK 200 FOR 1TN3 THE RANDOMIZED LOOPS WAS REMOVED FROM TEH SEARCH MODEL. REMARK 200 THESE LOOP IS 116-122 (LOOP 1) AND 145-150 (LOOP 4) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 0.35M MGAC, 20% 2-PROPANOL, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.58600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 74.58600 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 74.58600 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 74.58600 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 74.58600 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 74.58600 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 APPLY THE FOLLOWING TO CHAINS: C, T 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH T 200 LIES ON A SPECIAL POSITION. REMARK 375 HOH T 283 LIES ON A SPECIAL POSITION. REMARK 375 HOH T 284 LIES ON A SPECIAL POSITION. 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 LYS C 53 REMARK 465 GLY C 54 REMARK 465 THR C 55 REMARK 465 LYS C 56 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 LEU C 46 CG CD1 CD2 REMARK 470 LEU C 51 CG CD1 CD2 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 HOH T 174 O HOH T 244 1.85 REMARK 500 O HOH C 226 O HOH C 227 1.92 REMARK 500 O HOH C 224 O HOH C 225 2.04 REMARK 500 O HOH C 10 O HOH T 257 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH T 206 O HOH T 217 2665 1.96 REMARK 500 O HOH T 217 O HOH T 217 2665 1.99 REMARK 500 O HOH T 218 O HOH T 218 2665 2.14 REMARK 500 O HOH T 201 O HOH T 201 2665 2.18 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 ARG C 120 -50.97 77.62 REMARK 500 ASN C 135 45.41 -140.65 REMARK 500 LEU T 37 79.17 -159.74 REMARK 500 TYR T 87 -6.69 75.37 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 MG C 497 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 202 O REMARK 620 2 HOH C 210 O 90.2 REMARK 620 3 HOH C 221 O 171.2 86.1 REMARK 620 4 HOH C 245 O 95.2 172.3 89.3 REMARK 620 5 HOH C 246 O 92.7 92.8 95.5 81.5 REMARK 620 6 HOH C 251 O 90.3 96.2 82.2 89.2 170.4 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 MG C 497 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE NUMBER 52 IS SIMPLY SKIPPED IN CHAIN C. DBREF 3L9J C 46 180 PDB 3L9J 3L9J 46 180 DBREF 3L9J T 9 157 UNP P01375 TNFA_HUMAN 85 233 SEQRES 1 C 134 LEU GLN THR VAL CYS LEU LYS GLY THR LYS HIS MET LYS SEQRES 2 C 134 CYS PHE LEU ALA PHE THR GLN THR LYS THR PHE HIS GLU SEQRES 3 C 134 ALA SER GLU ASP CYS ILE SER ARG GLY GLY THR LEU SER SEQRES 4 C 134 THR PRO GLN THR GLY SER GLU ASN ASP ALA LEU TYR GLU SEQRES 5 C 134 TYR LEU ARG GLN SER VAL GLY ASN GLU ALA GLU ILE TRP SEQRES 6 C 134 LEU GLY LEU ASN LYS ARG TRP SER ARG TYR PHE TRP VAL SEQRES 7 C 134 ASP MET THR GLY THR ARG ILE ALA TYR LYS ASN TRP GLU SEQRES 8 C 134 HIS SER SER ASP ALA GLN PRO ASP PRO SER ASN TRP GLU SEQRES 9 C 134 ASN CYS ALA VAL LEU SER GLY ALA ALA ASN GLY LYS TRP SEQRES 10 C 134 PHE GLY LYS ARG CYS ARG ASP GLN LEU PRO TYR ILE CYS SEQRES 11 C 134 GLN PHE GLY ILE SEQRES 1 T 149 SER ASP LYS PRO VAL ALA HIS VAL VAL ALA ASN PRO GLN SEQRES 2 T 149 ALA GLU GLY GLN LEU GLN TRP LEU ASN ARG ARG ALA ASN SEQRES 3 T 149 ALA LEU LEU ALA ASN GLY VAL GLU LEU ARG ASP ASN GLN SEQRES 4 T 149 LEU VAL VAL PRO SER GLU GLY LEU TYR LEU ILE TYR SER SEQRES 5 T 149 GLN VAL LEU PHE LYS GLY GLN GLY CYS PRO SER THR HIS SEQRES 6 T 149 VAL LEU LEU THR HIS THR ILE SER ARG ILE ALA VAL SER SEQRES 7 T 149 TYR GLN THR LYS VAL ASN LEU LEU SER ALA ILE LYS SER SEQRES 8 T 149 PRO CYS GLN ARG GLU THR PRO GLU GLY ALA GLU ALA LYS SEQRES 9 T 149 PRO TRP TYR GLU PRO ILE TYR LEU GLY GLY VAL PHE GLN SEQRES 10 T 149 LEU GLU LYS GLY ASP ARG LEU SER ALA GLU ILE ASN ARG SEQRES 11 T 149 PRO ASP TYR LEU ASP PHE ALA GLU SER GLY GLN VAL TYR SEQRES 12 T 149 PHE GLY ILE ILE ALA LEU HET MG C 497 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 HOH *246(H2 O) HELIX 1 1 THR C 69 ARG C 80 1 12 HELIX 2 2 THR C 89 VAL C 104 1 16 HELIX 3 3 HIS C 138 GLN C 143 1 6 HELIX 4 4 ARG T 138 LEU T 142 5 5 SHEET 1 A 4 VAL C 49 LEU C 51 0 SHEET 2 A 4 MET C 58 LYS C 68 -1 O PHE C 61 N VAL C 49 SHEET 3 A 4 LEU C 172 ILE C 180 -1 O CYS C 176 N LEU C 62 SHEET 4 A 4 THR C 83 LEU C 84 -1 N THR C 83 O GLN C 177 SHEET 1 B 3 GLU C 109 TRP C 111 0 SHEET 2 B 3 CYS C 152 SER C 156 -1 O LEU C 155 N ILE C 110 SHEET 3 B 3 TRP C 163 LYS C 166 -1 O PHE C 164 N VAL C 154 SHEET 1 C 2 LEU C 114 ASN C 115 0 SHEET 2 C 2 VAL C 124 ASP C 125 -1 O VAL C 124 N ASN C 115 SHEET 1 D 3 TRP T 28 LEU T 29 0 SHEET 2 D 3 VAL T 13 ALA T 18 -1 N VAL T 17 O LEU T 29 SHEET 3 D 3 LEU T 36 ALA T 38 -1 O ALA T 38 N VAL T 13 SHEET 1 E 5 TRP T 28 LEU T 29 0 SHEET 2 E 5 VAL T 13 ALA T 18 -1 N VAL T 17 O LEU T 29 SHEET 3 E 5 TYR T 151 ALA T 156 -1 O PHE T 152 N VAL T 16 SHEET 4 E 5 GLY T 54 GLN T 67 -1 N TYR T 59 O GLY T 153 SHEET 5 E 5 PRO T 113 LEU T 126 -1 O GLY T 122 N ILE T 58 SHEET 1 F 5 GLU T 42 ARG T 44 0 SHEET 2 F 5 GLN T 47 VAL T 49 -1 O VAL T 49 N GLU T 42 SHEET 3 F 5 ARG T 131 ILE T 136 -1 O LEU T 132 N LEU T 48 SHEET 4 F 5 LEU T 76 ILE T 83 -1 N ILE T 83 O ARG T 131 SHEET 5 F 5 LYS T 90 LYS T 98 -1 O LYS T 98 N LEU T 76 SSBOND 1 CYS C 50 CYS C 60 1555 1555 2.08 SSBOND 2 CYS C 77 CYS C 176 1555 1555 2.03 SSBOND 3 CYS C 152 CYS C 168 1555 1555 2.06 SSBOND 4 CYS T 69 CYS T 101 1555 1555 2.09 LINK O HOH C 202 MG MG C 497 1555 1555 2.31 LINK O HOH C 210 MG MG C 497 1555 1555 1.95 LINK O HOH C 221 MG MG C 497 1555 1555 2.14 LINK O HOH C 245 MG MG C 497 1555 1555 2.63 LINK O HOH C 246 MG MG C 497 1555 1555 1.94 LINK O HOH C 251 MG MG C 497 1555 1555 2.07 SITE 1 AC1 6 HOH C 202 HOH C 210 HOH C 221 HOH C 245 SITE 2 AC1 6 HOH C 246 HOH C 251 CRYST1 83.905 83.905 149.172 90.00 90.00 120.00 P 63 2 2 12 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 0.011918 0.006881 0.000000 0.00000 SCALE2 0.000000 0.013762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006704 0.00000