PDB Short entry for 5DMI HEADER IMMUNE SYSTEM/SIGNALING PROTEIN 08-SEP-15 5DMI TITLE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH TITLE 2 CHI220 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN RESIDUES 23-193; COMPND 5 SYNONYM: B-CELL SURFACE ANTIGEN CD40,BP50,CD40L RECEPTOR,CDW40; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CHI220 FAB HEAVY CHAIN; COMPND 9 CHAIN: H; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: CHI220 FAB LIGHT CHAIN; COMPND 13 CHAIN: L; 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: CD40, TNFRSF5; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 10090, 9606; SOURCE 13 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 10090, 9606; SOURCE 19 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS CELL SURFACE RECEPTOR, ANTIBODY-ANTIGEN COMPLEX, ANTITUMOR, IMMUNE KEYWDS 2 SYSTEM-SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.SHERIFF REVDAT 3 20-JUL-16 5DMI 1 JRNL REVDAT 2 08-JUN-16 5DMI 1 JRNL REVDAT 1 01-JUN-16 5DMI 0 JRNL AUTH A.P.YAMNIUK,A.SURI,S.R.KRYSTEK,J.TAMURA,V.RAMAMURTHY,R.KUHN, JRNL AUTH 2 K.CARROLL,C.FLEENER,R.RYSECK,L.CHENG,Y.AN,P.DREW,S.GRANT, JRNL AUTH 3 S.J.SUCHARD,S.G.NADLER,J.W.BRYSON,S.SHERIFF JRNL TITL FUNCTIONAL ANTAGONISM OF HUMAN CD40 ACHIEVED BY TARGETING A JRNL TITL 2 UNIQUE SPECIES-SPECIFIC EPITOPE. JRNL REF J.MOL.BIOL. V. 428 2860 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27216500 JRNL DOI 10.1016/J.JMB.2016.05.014 REMARK 2 REMARK 2 RESOLUTION. 3.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.6 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14605 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 734 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 : 7 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.69 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.89 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2937 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1750 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2785 REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE : 0.2283 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.18 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 152 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 : 4001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.90030 REMARK 3 B22 (A**2) : -8.90030 REMARK 3 B33 (A**2) : 17.80050 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.372 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.397 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.900 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.868 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4115 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5615 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1329 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 88 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 604 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4115 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 554 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4626 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.39 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.18 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 25.24 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5DMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14668 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.690 REMARK 200 RESOLUTION RANGE LOW (A) : 201.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.24900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 16.30 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.800 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: CD40 ENSEMBLE FROM 1JMA, 2UWI, 2AW2, 1NCF, 1TNR, REMARK 200 2HEV, 2HEY; VL FROM 3D85; VH FROM 2ZPK; CL:CH1 FROM 2O5X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80MM SODIYM ACETATE, PH 4.6, 1.6 M REMARK 280 AMMONIUM SULFATE, 20% (V/V) GLYCEROL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z 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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 100.57600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 100.57600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.90450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 100.57600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 100.57600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.90450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 100.57600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 100.57600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.90450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 100.57600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 100.57600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.90450 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 PRO A 23 REMARK 465 HIS A 122 REMARK 465 ARG A 123 REMARK 465 SER A 124 REMARK 465 CYS A 125 REMARK 465 SER A 126 REMARK 465 PRO A 127 REMARK 465 GLY A 128 REMARK 465 PHE A 129 REMARK 465 GLY A 130 REMARK 465 VAL A 131 REMARK 465 LYS A 132 REMARK 465 GLN A 133 REMARK 465 ILE A 134 REMARK 465 ALA A 135 REMARK 465 THR A 136 REMARK 465 GLY A 137 REMARK 465 VAL A 138 REMARK 465 SER A 139 REMARK 465 ASP A 140 REMARK 465 THR A 141 REMARK 465 ILE A 142 REMARK 465 CYS A 143 REMARK 465 GLU A 144 REMARK 465 PRO A 145 REMARK 465 CYS A 146 REMARK 465 PRO A 147 REMARK 465 VAL A 148 REMARK 465 GLY A 149 REMARK 465 PHE A 150 REMARK 465 PHE A 151 REMARK 465 SER A 152 REMARK 465 ASP A 153 REMARK 465 VAL A 154 REMARK 465 SER A 155 REMARK 465 SER A 156 REMARK 465 ALA A 157 REMARK 465 PHE A 158 REMARK 465 GLU A 159 REMARK 465 LYS A 160 REMARK 465 CYS A 161 REMARK 465 HIS A 162 REMARK 465 PRO A 163 REMARK 465 TRP A 164 REMARK 465 THR A 165 REMARK 465 SER A 166 REMARK 465 CYS A 167 REMARK 465 GLU A 168 REMARK 465 THR A 169 REMARK 465 LYS A 170 REMARK 465 ASP A 171 REMARK 465 LEU A 172 REMARK 465 VAL A 173 REMARK 465 VAL A 174 REMARK 465 GLN A 175 REMARK 465 GLN A 176 REMARK 465 ALA A 177 REMARK 465 GLY A 178 REMARK 465 THR A 179 REMARK 465 ASP A 180 REMARK 465 LYS A 181 REMARK 465 THR A 182 REMARK 465 ASP A 183 REMARK 465 VAL A 184 REMARK 465 VAL A 185 REMARK 465 CYS A 186 REMARK 465 GLY A 187 REMARK 465 PRO A 188 REMARK 465 GLN A 189 REMARK 465 ASP A 190 REMARK 465 ARG A 191 REMARK 465 LEU A 192 REMARK 465 ARG A 193 REMARK 465 ASP A 194 REMARK 465 PRO A 195 REMARK 465 GLY A 196 REMARK 465 GLY A 197 REMARK 465 GLY A 198 REMARK 465 GLY A 199 REMARK 465 GLY A 200 REMARK 465 ARG A 201 REMARK 465 LEU A 202 REMARK 465 VAL A 203 REMARK 465 PRO A 204 REMARK 465 ARG A 205 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 GLU A 28 CG CD OE1 OE2 REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 TYR A 31 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 GLN A 79 CG CD OE1 NE2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ILE A 102 CG1 CG2 CD1 REMARK 470 THR A 104 OG1 CG2 REMARK 470 HIS A 110 CG ND1 CD2 CE1 NE2 REMARK 470 THR A 112 OG1 CG2 REMARK 470 SER A 113 OG REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 SER A 118 OG REMARK 470 LYS H 58 CG CD CE NZ REMARK 470 SER H 127 OG REMARK 470 SER H 128 OG REMARK 470 LYS H 129 CG CD CE NZ REMARK 470 SER H 130 OG REMARK 470 LYS H 222 CG CD CE NZ REMARK 470 VAL H 225 CG1 CG2 REMARK 470 LYS H 228 CG CD CE NZ REMARK 470 HIS L 41 CG ND1 CD2 CE1 NE2 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 LEU A 32 N - CA - C ANGL. DEV. = -20.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 25 -130.39 76.60 REMARK 500 CYS A 26 103.60 101.57 REMARK 500 GLN A 30 -47.94 -150.81 REMARK 500 TYR A 31 107.15 -33.01 REMARK 500 LEU A 32 116.43 -160.96 REMARK 500 ASN A 34 83.86 -158.61 REMARK 500 SER A 35 -37.04 86.87 REMARK 500 PHE A 54 46.43 -140.74 REMARK 500 GLU A 58 -84.62 -78.42 REMARK 500 CYS A 59 125.01 62.88 REMARK 500 SER A 65 -6.98 86.67 REMARK 500 TYR A 82 -75.79 88.74 REMARK 500 CYS A 83 73.70 81.75 REMARK 500 GLU A 107 32.46 -74.39 REMARK 500 GLU A 114 62.70 -3.30 REMARK 500 ALA A 115 99.44 62.83 REMARK 500 CYS A 116 71.89 169.45 REMARK 500 LYS H 43 -176.26 -41.53 REMARK 500 SER H 95 146.10 97.17 REMARK 500 ASN H 99 61.34 -106.02 REMARK 500 ASP H 100A -83.14 -52.94 REMARK 500 LEU H 100B 99.07 44.66 REMARK 500 SER H 128 -47.78 71.75 REMARK 500 SER H 132 -77.45 -79.49 REMARK 500 ASP H 146 85.50 35.43 REMARK 500 THR H 167 -56.40 -121.24 REMARK 500 SER H 181 -9.83 -54.59 REMARK 500 ASN H 216 56.05 38.66 REMARK 500 VAL H 225 -94.61 51.75 REMARK 500 GLU H 226 131.06 66.69 REMARK 500 SER L 30 -109.87 52.48 REMARK 500 ALA L 51 -45.43 64.05 REMARK 500 VAL L 78 122.20 -22.30 REMARK 500 ASP L 82 15.80 -67.42 REMARK 500 HIS L 92 73.47 -65.01 REMARK 500 SER L 93 138.77 102.92 REMARK 500 THR L 102 89.49 41.54 REMARK 500 ASN L 138 92.47 41.94 REMARK 500 ASN L 152 17.40 53.02 REMARK 500 ASN L 158 25.58 -154.69 REMARK 500 LYS L 169 -64.95 -104.30 REMARK 500 SER L 171 21.71 43.32 REMARK 500 LYS L 190 -42.25 -137.77 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 SO4 H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 L 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DMJ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR STATES THAT THE PROTEIN WAS EXPRESSED WITH ASN153 AND REMARK 999 ASN180 (AND POST-TRANSLATIONAL CARBOHYDRATE) AND THEN SUBJECTED TO REMARK 999 PNGASE F CLEAVAGE WHICH REMOVES THE CARBOHYDRATE AND LEAVES ASP153 REMARK 999 AND ASP180 RATHER THAN ASN DBREF 5DMI A 23 193 UNP P25942 TNR5_HUMAN 23 193 DBREF 5DMI H 1 228 PDB 5DMI 5DMI 1 228 DBREF 5DMI L 1 213 PDB 5DMI 5DMI 1 213 SEQADV 5DMI ASP A 153 UNP P25942 ASN 153 SEE REMARK 999 SEQADV 5DMI ASP A 180 UNP P25942 ASN 180 SEE REMARK 999 SEQADV 5DMI ASP A 194 UNP P25942 EXPRESSION TAG SEQADV 5DMI PRO A 195 UNP P25942 EXPRESSION TAG SEQADV 5DMI GLY A 196 UNP P25942 EXPRESSION TAG SEQADV 5DMI GLY A 197 UNP P25942 EXPRESSION TAG SEQADV 5DMI GLY A 198 UNP P25942 EXPRESSION TAG SEQADV 5DMI GLY A 199 UNP P25942 EXPRESSION TAG SEQADV 5DMI GLY A 200 UNP P25942 EXPRESSION TAG SEQADV 5DMI ARG A 201 UNP P25942 EXPRESSION TAG SEQADV 5DMI LEU A 202 UNP P25942 EXPRESSION TAG SEQADV 5DMI VAL A 203 UNP P25942 EXPRESSION TAG SEQADV 5DMI PRO A 204 UNP P25942 EXPRESSION TAG SEQADV 5DMI ARG A 205 UNP P25942 EXPRESSION TAG SEQRES 1 A 183 PRO THR ALA CYS ARG GLU LYS GLN TYR LEU ILE ASN SER SEQRES 2 A 183 GLN CYS CYS SER LEU CYS GLN PRO GLY GLN LYS LEU VAL SEQRES 3 A 183 SER ASP CYS THR GLU PHE THR GLU THR GLU CYS LEU PRO SEQRES 4 A 183 CYS GLY GLU SER GLU PHE LEU ASP THR TRP ASN ARG GLU SEQRES 5 A 183 THR HIS CYS HIS GLN HIS LYS TYR CYS ASP PRO ASN LEU SEQRES 6 A 183 GLY LEU ARG VAL GLN GLN LYS GLY THR SER GLU THR ASP SEQRES 7 A 183 THR ILE CYS THR CYS GLU GLU GLY TRP HIS CYS THR SER SEQRES 8 A 183 GLU ALA CYS GLU SER CYS VAL LEU HIS ARG SER CYS SER SEQRES 9 A 183 PRO GLY PHE GLY VAL LYS GLN ILE ALA THR GLY VAL SER SEQRES 10 A 183 ASP THR ILE CYS GLU PRO CYS PRO VAL GLY PHE PHE SER SEQRES 11 A 183 ASP VAL SER SER ALA PHE GLU LYS CYS HIS PRO TRP THR SEQRES 12 A 183 SER CYS GLU THR LYS ASP LEU VAL VAL GLN GLN ALA GLY SEQRES 13 A 183 THR ASP LYS THR ASP VAL VAL CYS GLY PRO GLN ASP ARG SEQRES 14 A 183 LEU ARG ASP PRO GLY GLY GLY GLY GLY ARG LEU VAL PRO SEQRES 15 A 183 ARG SEQRES 1 H 223 GLN ILE GLN LEU VAL GLN SER GLY PRO GLU LEU LYS LYS SEQRES 2 H 223 PRO GLY GLU THR VAL ARG ILE SER CYS LYS ALA SER GLY SEQRES 3 H 223 TYR ALA PHE THR THR THR GLY MET GLN TRP VAL GLN GLU SEQRES 4 H 223 MET PRO GLY LYS GLY LEU LYS TRP ILE GLY TRP ILE ASN SEQRES 5 H 223 THR HIS SER GLY VAL PRO LYS TYR VAL GLU ASP PHE LYS SEQRES 6 H 223 GLY ARG PHE ALA PHE SER LEU GLU THR SER ALA ASN THR SEQRES 7 H 223 ALA TYR LEU GLN ILE SER ASN LEU LYS ASN GLU ASP THR SEQRES 8 H 223 ALA THR TYR PHE CYS VAL ARG SER GLY ASN GLY ASN TYR SEQRES 9 H 223 ASP LEU ALA TYR PHE ALA TYR TRP GLY GLN GLY THR LEU SEQRES 10 H 223 VAL THR VAL SER ALA ALA SER THR LYS GLY PRO SER VAL SEQRES 11 H 223 PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY SEQRES 12 H 223 THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO SEQRES 13 H 223 GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SEQRES 14 H 223 SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER SEQRES 15 H 223 GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SEQRES 16 H 223 SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN SEQRES 17 H 223 HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU SEQRES 18 H 223 PRO LYS SEQRES 1 L 213 ASP ILE VAL LEU THR GLN SER PRO ALA THR LEU SER VAL SEQRES 2 L 213 THR PRO GLY ASP ARG VAL SER LEU SER CYS ARG ALA SER SEQRES 3 L 213 GLN SER ILE SER ASP TYR LEU HIS TRP TYR GLN GLN LYS SEQRES 4 L 213 SER HIS GLU SER PRO ARG LEU LEU ILE LYS TYR ALA SER SEQRES 5 L 213 HIS SER ILE SER GLY ILE PRO SER ARG PHE SER GLY SER SEQRES 6 L 213 GLY SER GLY SER ASP PHE THR LEU SER ILE ASN SER VAL SEQRES 7 L 213 GLU PRO GLU ASP VAL GLY ILE TYR TYR CYS GLN HIS GLY SEQRES 8 L 213 HIS SER PHE PRO TRP THR PHE GLY GLY GLY THR LYS LEU 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 HET SO4 H 301 5 HET SO4 L 301 5 HETNAM SO4 SULFATE ION FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *(H2 O) HELIX 1 AA1 ASP A 84 GLY A 88 5 5 HELIX 2 AA2 THR H 73 ALA H 75 5 3 HELIX 3 AA3 LYS H 83 THR H 87 5 5 HELIX 4 AA4 SER H 196 GLN H 204 1 6 HELIX 5 AA5 LYS H 213 ASN H 216 5 4 HELIX 6 AA6 SER L 121 GLY L 128 1 8 HELIX 7 AA7 LYS L 183 HIS L 189 1 7 SHEET 1 AA1 2 GLN A 45 LYS A 46 0 SHEET 2 AA1 2 LEU A 60 PRO A 61 -1 O LEU A 60 N LYS A 46 SHEET 1 AA2 2 GLU A 66 PHE A 67 0 SHEET 2 AA2 2 HIS A 78 GLN A 79 -1 O HIS A 78 N PHE A 67 SHEET 1 AA3 2 HIS A 110 CYS A 111 0 SHEET 2 AA3 2 CYS A 119 VAL A 120 -1 O VAL A 120 N HIS A 110 SHEET 1 AA4 4 GLN H 3 GLN H 6 0 SHEET 2 AA4 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA4 4 THR H 77 ILE H 82 -1 O LEU H 80 N ILE H 20 SHEET 4 AA4 4 PHE H 67 GLU H 72 -1 N SER H 70 O TYR H 79 SHEET 1 AA5 6 GLU H 10 LYS H 12 0 SHEET 2 AA5 6 THR H 107 VAL H 111 1 O THR H 110 N LYS H 12 SHEET 3 AA5 6 ALA H 88 ARG H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 AA5 6 MET H 34 GLU H 39 -1 N VAL H 37 O PHE H 91 SHEET 5 AA5 6 LEU H 45 ILE H 51 -1 O ILE H 51 N MET H 34 SHEET 6 AA5 6 PRO H 57 TYR H 59 -1 O LYS H 58 N TRP H 50 SHEET 1 AA6 4 GLU H 10 LYS H 12 0 SHEET 2 AA6 4 THR H 107 VAL H 111 1 O THR H 110 N LYS H 12 SHEET 3 AA6 4 ALA H 88 ARG H 94 -1 N ALA H 88 O VAL H 109 SHEET 4 AA6 4 TYR H 102 TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AA7 4 SER H 120 LEU H 124 0 SHEET 2 AA7 4 THR H 137 TYR H 147 -1 O LEU H 143 N PHE H 122 SHEET 3 AA7 4 TYR H 185 PRO H 194 -1 O LEU H 187 N VAL H 144 SHEET 4 AA7 4 VAL H 171 THR H 173 -1 N HIS H 172 O VAL H 190 SHEET 1 AA8 4 SER H 120 LEU H 124 0 SHEET 2 AA8 4 THR H 137 TYR H 147 -1 O LEU H 143 N PHE H 122 SHEET 3 AA8 4 TYR H 185 PRO H 194 -1 O LEU H 187 N VAL H 144 SHEET 4 AA8 4 VAL H 177 LEU H 178 -1 N VAL H 177 O SER H 186 SHEET 1 AA9 3 THR H 153 TRP H 157 0 SHEET 2 AA9 3 CYS H 208 HIS H 212 -1 O ASN H 209 N SER H 156 SHEET 3 AA9 3 THR H 217 LYS H 221 -1 O VAL H 219 N VAL H 210 SHEET 1 AB1 4 LEU L 4 THR L 5 0 SHEET 2 AB1 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB1 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 AB1 4 PHE L 62 SER L 67 -1 N SER L 63 O SER L 74 SHEET 1 AB2 6 THR L 10 VAL L 13 0 SHEET 2 AB2 6 LYS L 103 ILE L 106 1 O GLU L 105 N VAL L 13 SHEET 3 AB2 6 GLY L 84 HIS L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 AB2 6 LEU L 33 GLN L 38 -1 N GLN L 38 O ILE L 85 SHEET 5 AB2 6 ARG L 45 LYS L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AB2 6 HIS L 53 SER L 54 -1 O HIS L 53 N LYS L 49 SHEET 1 AB3 4 SER L 114 PHE L 118 0 SHEET 2 AB3 4 THR L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 AB3 4 TYR L 173 SER L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 AB3 4 SER L 159 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 AB4 4 ALA L 153 GLN L 155 0 SHEET 2 AB4 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 AB4 4 VAL L 191 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 AB4 4 VAL L 205 ASN L 210 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS A 26 CYS A 37 1555 1555 2.06 SSBOND 2 CYS A 38 CYS A 51 1555 1555 2.03 SSBOND 3 CYS A 41 CYS A 59 1555 1555 2.04 SSBOND 4 CYS A 62 CYS A 77 1555 1555 2.07 SSBOND 5 CYS A 83 CYS A 103 1555 1555 2.05 SSBOND 6 CYS A 105 CYS A 119 1555 1555 2.04 SSBOND 7 CYS A 111 CYS A 116 1555 1555 2.05 SSBOND 8 CYS H 22 CYS H 92 1555 1555 2.05 SSBOND 9 CYS H 142 CYS H 208 1555 1555 2.04 SSBOND 10 CYS L 23 CYS L 88 1555 1555 2.05 SSBOND 11 CYS L 134 CYS L 194 1555 1555 2.05 CISPEP 1 ALA A 115 CYS A 116 0 2.30 CISPEP 2 SER H 95 GLY H 96 0 4.04 CISPEP 3 PHE H 148 PRO H 149 0 -3.31 CISPEP 4 GLU H 150 PRO H 151 0 13.90 CISPEP 5 SER L 7 PRO L 8 0 3.68 CISPEP 6 PHE L 94 PRO L 95 0 -2.37 CISPEP 7 TYR L 140 PRO L 141 0 -3.16 SITE 1 AC1 2 ASP H 62 ARG H 66 SITE 1 AC2 2 HIS L 53 SER L 54 CRYST1 201.152 201.152 63.809 90.00 90.00 90.00 P 42 21 2 8 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 0.004971 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015672 0.00000