PDB Short entry for 3WD5 HEADER IMMUNE SYSTEM 06-JUN-13 3WD5 TITLE CRYSTAL STRUCTURE OF TNFALPHA IN COMPLEX WITH ADALIMUMAB FAB FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TUMOR NECROSIS FACTOR, SOLUBLE FORM; COMPND 5 SYNONYM: TNFALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ADALIMUMAB LIGHT CHAIN; COMPND 9 CHAIN: L; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: ADALIMUMAB HEAVY CHAIN; COMPND 13 CHAIN: H; COMPND 14 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: TNFA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS ANTIBODY BINDING EPITOPE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.HU,S.Y.LIANG,Y.J.GUO,Z.Y.LOU REVDAT 3 01-JUL-15 3WD5 1 JRNL REVDAT 2 21-AUG-13 3WD5 1 JRNL REVDAT 1 14-AUG-13 3WD5 0 JRNL AUTH S.HU,S.Y.LIANG,H.GUO,D.ZHANG,H.LI,X.WANG,W.YANG,W.QIAN, JRNL AUTH 2 S.HOU,H.WANG,Y.J.GUO,Z.Y.LOU JRNL TITL COMPARISON OF THE INHIBITION MECHANISMS OF ADALIMUMAB AND JRNL TITL 2 INFLIXIMAB IN TREATING TUMOR NECROSIS FACTOR JRNL TITL 3 ALPHA-ASSOCIATED DISEASES FROM A MOLECULAR VIEW JRNL REF J.BIOL.CHEM. V. 288 27059 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23943614 JRNL DOI 10.1074/JBC.M113.491530 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12943 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.2602 - 5.3001 1.00 2544 130 0.2131 0.2585 REMARK 3 2 5.3001 - 4.2080 1.00 2462 124 0.1554 0.2313 REMARK 3 3 4.2080 - 3.6764 1.00 2429 138 0.1705 0.2515 REMARK 3 4 3.6764 - 3.3404 1.00 2440 121 0.1899 0.3576 REMARK 3 5 3.3404 - 3.1010 1.00 2422 133 0.2119 0.3461 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.06 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 4536 REMARK 3 ANGLE : 1.447 6168 REMARK 3 CHIRALITY : 0.113 697 REMARK 3 PLANARITY : 0.006 795 REMARK 3 DIHEDRAL : 17.883 1630 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3WD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUN-13. REMARK 100 THE RCSB ID CODE IS RCSB096185. 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 : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12943 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 43.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 26.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG400, 0.1M SODIUM ACETATE REMARK 280 TRIHYDRATE, 0.1M CADMIUM CHLORIDE HYDRATE, PH 4.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y,-Z REMARK 290 16555 X,-Y,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z,-X,-Y+1/2 REMARK 290 19555 -Z,-X+1/2,Y REMARK 290 20555 -Z+1/2,X,-Y REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z,-X REMARK 290 23555 Y,-Z,-X+1/2 REMARK 290 24555 -Y,-Z+1/2,X 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 80.92450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.92450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 80.92450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.92450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 80.92450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 80.92450 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 80.92450 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 80.92450 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 80.92450 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 80.92450 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 80.92450 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 80.92450 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 80.92450 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 80.92450 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 80.92450 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 80.92450 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 80.92450 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 80.92450 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 80.92450 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 80.92450 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 80.92450 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 80.92450 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 80.92450 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 80.92450 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 80.92450 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 80.92450 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 0.00000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L, H 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 A 201 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 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 LYS H 137 REMARK 465 SER H 138 REMARK 465 THR H 139 REMARK 465 SER H 140 REMARK 465 GLY H 141 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS L 45 CE REMARK 480 GLU L 81 CG REMARK 480 GLN L 100 CG REMARK 480 LYS L 126 CE NZ REMARK 480 GLN L 147 CG REMARK 480 LEU L 154 CD1 CD2 REMARK 480 LYS L 169 CG CD CE REMARK 480 LYS L 188 NZ REMARK 480 ARG L 211 NH2 REMARK 480 GLY L 212 CA REMARK 480 GLU L 213 CA O CB CG REMARK 480 GLU H 1 OE2 REMARK 480 PRO H 41 CA REMARK 480 GLU H 89 CG REMARK 480 SER H 135 CA CB REMARK 480 SER H 136 CB REMARK 480 GLY H 142 CA REMARK 480 SER H 196 N REMARK 480 GLY H 198 CA REMARK 480 LYS H 209 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 69 CB CYS A 101 1.75 REMARK 500 OD2 ASP H 59 O HOH H 303 2.06 REMARK 500 O ALA A 145 O HOH H 303 2.07 REMARK 500 OD1 ASP H 30 O HOH H 305 2.15 REMARK 500 O ALA H 61 N SER H 63 2.17 REMARK 500 O VAL H 64 N GLY H 66 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 SER A 9 130.77 95.62 REMARK 500 ALA A 33 -137.08 22.15 REMARK 500 LEU A 37 88.08 -179.36 REMARK 500 ARG A 44 -68.46 -126.68 REMARK 500 ASP A 45 47.82 -106.53 REMARK 500 PRO A 70 -126.32 -106.35 REMARK 500 THR A 72 -46.51 3.53 REMARK 500 SER A 86 -72.99 -86.94 REMARK 500 TYR A 87 80.09 -57.98 REMARK 500 GLN A 88 2.89 -56.83 REMARK 500 ALA A 96 135.95 -175.10 REMARK 500 CYS A 101 104.28 2.31 REMARK 500 ARG A 103 -29.13 41.98 REMARK 500 GLU A 104 -51.90 -4.51 REMARK 500 THR A 105 79.92 37.57 REMARK 500 PRO A 106 49.56 -60.27 REMARK 500 ALA A 109 -173.70 -170.26 REMARK 500 GLU A 110 121.31 69.19 REMARK 500 SER A 147 -79.11 -52.47 REMARK 500 ILE L 2 124.98 75.57 REMARK 500 ARG L 30 -124.49 54.88 REMARK 500 ALA L 51 -30.92 72.77 REMARK 500 SER L 52 -16.77 -140.13 REMARK 500 SER L 77 88.36 -156.66 REMARK 500 ARG L 93 109.62 81.01 REMARK 500 LYS L 107 -89.34 -55.22 REMARK 500 ARG L 108 157.97 30.26 REMARK 500 ASN L 152 14.61 59.68 REMARK 500 ARG H 16 -150.90 -76.16 REMARK 500 ASP H 62 62.12 -43.87 REMARK 500 SER H 63 -8.42 173.48 REMARK 500 VAL H 64 -72.84 -142.46 REMARK 500 GLU H 65 -61.81 35.11 REMARK 500 ARG H 72 114.11 -165.64 REMARK 500 LEU H 102 -81.51 57.26 REMARK 500 ALA H 122 -142.34 -70.77 REMARK 500 ASP H 152 62.54 60.64 REMARK 500 ALA H 166 15.92 -59.81 REMARK 500 LEU H 167 109.15 -160.68 REMARK 500 SER H 194 -6.73 -54.63 REMARK 500 SER H 195 -60.70 -103.32 REMARK 500 SER H 196 45.68 -59.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN L 92 16.6 L L OUTSIDE RANGE REMARK 500 ARG L 93 16.3 L L OUTSIDE RANGE REMARK 500 ARG L 108 24.2 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G3Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TNFALPHA IN COMPLEX WITH INFLIXIMAB REMARK 900 FAB FRAGMENT DBREF 3WD5 A 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 3WD5 L 1 213 PDB 3WD5 3WD5 1 213 DBREF 3WD5 H 1 219 PDB 3WD5 3WD5 1 219 SEQADV 3WD5 ASP A 31 UNP P01375 ARG 107 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 ASP 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 L 213 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 213 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 213 GLN GLY ILE ARG ASN TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 213 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 L 213 THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 213 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 213 GLN PRO GLU ASP VAL ALA THR TYR TYR CYS GLN ARG TYR SEQRES 8 L 213 ASN ARG ALA PRO TYR THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 L 213 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 213 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 213 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 213 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 213 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 213 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 213 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 213 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 213 PHE ASN ARG GLY GLU SEQRES 1 H 219 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 219 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 219 PHE THR PHE ASP ASP TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 H 219 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ALA ILE THR SEQRES 5 H 219 TRP ASN SER GLY HIS ILE ASP TYR ALA ASP SER VAL GLU SEQRES 6 H 219 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 219 LEU TYR LEU ASP MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 219 ALA VAL TYR TYR CYS ALA LYS VAL SER TYR LEU SER THR SEQRES 9 H 219 ALA SER SER LEU ASP TYR TRP GLY GLN GLY THR LEU VAL SEQRES 10 H 219 THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE SEQRES 11 H 219 PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR SEQRES 12 H 219 ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU SEQRES 13 H 219 PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER SEQRES 14 H 219 GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY SEQRES 15 H 219 LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SEQRES 16 H 219 SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS SEQRES 17 H 219 LYS PRO SER ASN THR LYS VAL ASP LYS LYS ILE FORMUL 4 HOH *34(H2 O) HELIX 1 1 ARG A 138 LEU A 142 5 5 HELIX 2 2 GLU A 146 GLN A 149 5 4 HELIX 3 3 GLN L 79 VAL L 83 5 5 HELIX 4 4 SER L 121 GLY L 128 1 8 HELIX 5 5 LYS L 183 GLU L 187 1 5 HELIX 6 6 THR H 28 TYR H 32 5 5 HELIX 7 7 ARG H 87 THR H 91 5 5 HELIX 8 8 SER H 164 ALA H 166 5 3 SHEET 1 A 3 TRP A 28 LEU A 29 0 SHEET 2 A 3 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 A 3 LEU A 36 ALA A 38 -1 O ALA A 38 N VAL A 13 SHEET 1 B 5 TRP A 28 LEU A 29 0 SHEET 2 B 5 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29 SHEET 3 B 5 TYR A 151 LEU A 157 -1 O PHE A 152 N VAL A 16 SHEET 4 B 5 GLY A 54 GLN A 67 -1 N TYR A 59 O GLY A 153 SHEET 5 B 5 PRO A 113 LEU A 126 -1 O TRP A 114 N GLY A 66 SHEET 1 C 5 GLU A 42 LEU A 43 0 SHEET 2 C 5 LEU A 48 VAL A 49 -1 O VAL A 49 N GLU A 42 SHEET 3 C 5 ARG A 131 ILE A 136 -1 O LEU A 132 N LEU A 48 SHEET 4 C 5 LEU A 76 ILE A 83 -1 N ILE A 83 O ARG A 131 SHEET 5 C 5 LYS A 90 LYS A 98 -1 O LEU A 93 N ILE A 80 SHEET 1 D 4 MET L 4 SER L 7 0 SHEET 2 D 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 D 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 D 4 PHE L 62 SER L 63 -1 N SER L 63 O THR L 74 SHEET 1 E 6 SER L 10 ALA L 13 0 SHEET 2 E 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 E 6 THR L 85 ARG L 90 -1 N TYR L 86 O THR L 102 SHEET 4 E 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 E 6 LYS L 45 TYR L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 E 6 THR L 53 LEU L 54 -1 O THR L 53 N TYR L 49 SHEET 1 F 3 SER L 114 PHE L 118 0 SHEET 2 F 3 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 F 3 TYR L 173 SER L 182 -1 O TYR L 173 N PHE L 139 SHEET 1 G 4 ALA L 153 LEU L 154 0 SHEET 2 G 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 G 4 VAL L 191 THR L 197 -1 O ALA L 193 N LYS L 149 SHEET 4 G 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SHEET 1 H 4 GLN H 3 SER H 7 0 SHEET 2 H 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 H 4 SER H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 H 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 I 6 GLY H 10 VAL H 12 0 SHEET 2 I 6 LEU H 116 VAL H 119 1 O THR H 118 N GLY H 10 SHEET 3 I 6 ALA H 92 VAL H 99 -1 N ALA H 92 O VAL H 117 SHEET 4 I 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 I 6 LEU H 45 ILE H 51 -1 O SER H 49 N TRP H 36 SHEET 6 I 6 ILE H 58 TYR H 60 -1 O ASP H 59 N ALA H 50 SHEET 1 J 4 GLY H 10 VAL H 12 0 SHEET 2 J 4 LEU H 116 VAL H 119 1 O THR H 118 N GLY H 10 SHEET 3 J 4 ALA H 92 VAL H 99 -1 N ALA H 92 O VAL H 117 SHEET 4 J 4 LEU H 108 TRP H 111 -1 O TYR H 110 N LYS H 98 SHEET 1 K 4 SER H 128 LEU H 132 0 SHEET 2 K 4 THR H 143 TYR H 153 -1 O GLY H 147 N LEU H 132 SHEET 3 K 4 TYR H 184 PRO H 193 -1 O VAL H 190 N LEU H 146 SHEET 4 K 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 189 SHEET 1 L 4 SER H 128 LEU H 132 0 SHEET 2 L 4 THR H 143 TYR H 153 -1 O GLY H 147 N LEU H 132 SHEET 3 L 4 TYR H 184 PRO H 193 -1 O VAL H 190 N LEU H 146 SHEET 4 L 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 185 SHEET 1 M 3 THR H 159 TRP H 162 0 SHEET 2 M 3 TYR H 202 HIS H 208 -1 O ASN H 207 N THR H 159 SHEET 3 M 3 THR H 213 VAL H 215 -1 O THR H 213 N HIS H 208 SHEET 1 N 3 THR H 159 TRP H 162 0 SHEET 2 N 3 TYR H 202 HIS H 208 -1 O ASN H 207 N THR H 159 SHEET 3 N 3 LYS H 218 ILE H 219 -1 O ILE H 219 N TYR H 202 SSBOND 1 CYS A 69 CYS A 101 1555 1555 2.05 SSBOND 2 CYS L 23 CYS L 88 1555 1555 2.06 SSBOND 3 CYS L 134 CYS L 194 1555 1555 2.04 SSBOND 4 CYS H 22 CYS H 96 1555 1555 2.05 SSBOND 5 CYS H 148 CYS H 204 1555 1555 2.03 CISPEP 1 ARG A 6 THR A 7 0 13.50 CISPEP 2 SER L 7 PRO L 8 0 -2.24 CISPEP 3 ASN L 92 ARG L 93 0 -5.94 CISPEP 4 ALA L 94 PRO L 95 0 -4.86 CISPEP 5 TYR L 140 PRO L 141 0 5.44 CISPEP 6 PHE H 154 PRO H 155 0 -4.04 CISPEP 7 GLU H 156 PRO H 157 0 3.57 CRYST1 161.849 161.849 161.849 90.00 90.00 90.00 I 21 3 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 0.006179 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006179 0.00000