HEADER SIGNALING PROTEIN 09-JUL-20 6XQ1 TITLE RECEPTOR FOR ADVANCED GLYCATION END PRODUCTS VC1 DOMAIN IN COMPLEX TITLE 2 WITH 3-(3-((4-(4-CARBOXYPHENOXY)BENZYL)OXY)PHENYL)-1H-INDOLE-2- TITLE 3 CARBOXYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: VC1 DOMAIN, RESDUES 23-231; COMPND 5 SYNONYM: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS; COMPND 6 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: AGER, RAGE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAGE, INHIBITOR, RECEPTOR, ADVANCED GLYCATION END PRODUCTS, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.E.SALAY,N.KOZLYUK,B.A.GILSTON,R.D.GOGLIOTTI,P.P.CHRISTOV,K.KIM, AUTHOR 2 M.OVEE,A.G.WATERSON,W.J.CHAZIN REVDAT 7 18-OCT-23 6XQ1 1 REMARK REVDAT 6 15-DEC-21 6XQ1 1 AUTHOR JRNL REVDAT 5 20-OCT-21 6XQ1 1 JRNL REVDAT 4 11-AUG-21 6XQ1 1 REMARK REVDAT 3 04-AUG-21 6XQ1 1 JRNL REVDAT 2 28-JUL-21 6XQ1 1 JRNL REVDAT 1 14-JUL-21 6XQ1 0 JRNL AUTH N.KOZLYUK,B.A.GILSTON,L.E.SALAY,R.D.GOGLIOTTI,P.P.CHRISTOV, JRNL AUTH 2 K.KIM,M.OVEE,A.G.WATERSON,W.J.CHAZIN JRNL TITL A FRAGMENT-BASED APPROACH TO DISCOVERY OF RECEPTOR FOR JRNL TITL 2 ADVANCED GLYCATION END PRODUCTS INHIBITORS. JRNL REF PROTEINS V. 89 1399 2021 JRNL REFN ESSN 1097-0134 JRNL PMID 34156100 JRNL DOI 10.1002/PROT.26162 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 95281 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 4640 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 33.4500 - 4.6800 1.00 3073 168 0.1669 0.1833 REMARK 3 2 4.6800 - 3.7200 1.00 3076 142 0.1417 0.1629 REMARK 3 3 3.7200 - 3.2500 1.00 3075 135 0.1608 0.1610 REMARK 3 4 3.2500 - 2.9500 1.00 3000 172 0.1815 0.2129 REMARK 3 5 2.9500 - 2.7400 1.00 3039 165 0.1917 0.2145 REMARK 3 6 2.7400 - 2.5800 1.00 3041 151 0.1762 0.1795 REMARK 3 7 2.5800 - 2.4500 1.00 3011 167 0.1829 0.2132 REMARK 3 8 2.4500 - 2.3400 1.00 3057 137 0.1779 0.2000 REMARK 3 9 2.3400 - 2.2500 1.00 3042 144 0.1795 0.2159 REMARK 3 10 2.2500 - 2.1700 1.00 2996 157 0.1774 0.1956 REMARK 3 11 2.1700 - 2.1100 1.00 3058 151 0.1661 0.1966 REMARK 3 12 2.1100 - 2.0500 1.00 3000 139 0.1639 0.1980 REMARK 3 13 2.0500 - 1.9900 1.00 3037 171 0.1690 0.2141 REMARK 3 14 1.9900 - 1.9400 1.00 3029 163 0.1682 0.1810 REMARK 3 15 1.9400 - 1.9000 1.00 3033 133 0.1644 0.2263 REMARK 3 16 1.9000 - 1.8600 1.00 2963 173 0.1781 0.1992 REMARK 3 17 1.8600 - 1.8200 1.00 3072 154 0.1841 0.2381 REMARK 3 18 1.8200 - 1.7900 1.00 2980 161 0.1821 0.2203 REMARK 3 19 1.7900 - 1.7500 1.00 3070 135 0.1767 0.1988 REMARK 3 20 1.7500 - 1.7300 1.00 3065 132 0.1737 0.1861 REMARK 3 21 1.7300 - 1.7000 1.00 3006 128 0.1762 0.2289 REMARK 3 22 1.7000 - 1.6700 1.00 3004 151 0.1718 0.2250 REMARK 3 23 1.6700 - 1.6500 1.00 3042 134 0.1780 0.2151 REMARK 3 24 1.6500 - 1.6200 1.00 2970 179 0.1801 0.2255 REMARK 3 25 1.6200 - 1.6000 1.00 3069 143 0.1976 0.1898 REMARK 3 26 1.6000 - 1.5800 1.00 3011 177 0.2046 0.2192 REMARK 3 27 1.5800 - 1.5600 1.00 2974 186 0.2097 0.2734 REMARK 3 28 1.5600 - 1.5400 1.00 3007 163 0.2332 0.2803 REMARK 3 29 1.5400 - 1.5200 1.00 2962 177 0.2534 0.2973 REMARK 3 30 1.5200 - 1.5100 0.95 2879 152 0.2703 0.2988 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) : 0.162 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.748 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.12 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 : 0.017 3557 REMARK 3 ANGLE : 1.460 4889 REMARK 3 CHIRALITY : 0.099 513 REMARK 3 PLANARITY : 0.010 653 REMARK 3 DIHEDRAL : 20.447 519 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 20:118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -44.4978 -11.8403 22.1339 REMARK 3 T TENSOR REMARK 3 T11: 0.2335 T22: 0.1435 REMARK 3 T33: 0.1665 T12: 0.0881 REMARK 3 T13: -0.0104 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.8057 L22: 2.1753 REMARK 3 L33: 2.1740 L12: -0.3780 REMARK 3 L13: -0.1336 L23: 0.1655 REMARK 3 S TENSOR REMARK 3 S11: -0.1015 S12: -0.2591 S13: 0.0103 REMARK 3 S21: 0.3466 S22: 0.1275 S23: 0.0204 REMARK 3 S31: 0.2187 S32: 0.1452 S33: -0.0134 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 119:231 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.2274 -6.0940 -12.7674 REMARK 3 T TENSOR REMARK 3 T11: 0.2013 T22: 0.3018 REMARK 3 T33: 0.2701 T12: -0.0217 REMARK 3 T13: 0.0660 T23: -0.0838 REMARK 3 L TENSOR REMARK 3 L11: 2.4653 L22: 1.7643 REMARK 3 L33: 3.7995 L12: 0.8762 REMARK 3 L13: -2.1817 L23: -0.2377 REMARK 3 S TENSOR REMARK 3 S11: -0.0179 S12: -0.0376 S13: 0.0935 REMARK 3 S21: -0.2150 S22: 0.2808 S23: -0.3284 REMARK 3 S31: -0.0492 S32: 0.6472 S33: -0.1320 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND (RESID 20:118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.3439 -32.7006 17.8266 REMARK 3 T TENSOR REMARK 3 T11: 0.2406 T22: 0.1322 REMARK 3 T33: 0.1650 T12: 0.0808 REMARK 3 T13: 0.0086 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 1.7755 L22: 2.0209 REMARK 3 L33: 2.1333 L12: -0.4126 REMARK 3 L13: -0.0262 L23: 0.1919 REMARK 3 S TENSOR REMARK 3 S11: 0.1114 S12: 0.2235 S13: -0.0181 REMARK 3 S21: -0.3618 S22: -0.0835 S23: 0.0034 REMARK 3 S31: -0.2284 S32: -0.1080 S33: -0.0155 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESID 119:231 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.0988 -19.2924 52.8631 REMARK 3 T TENSOR REMARK 3 T11: 0.2687 T22: 0.2464 REMARK 3 T33: 0.2668 T12: -0.0596 REMARK 3 T13: 0.0431 T23: -0.1008 REMARK 3 L TENSOR REMARK 3 L11: 2.7020 L22: 1.6711 REMARK 3 L33: 4.1753 L12: 0.5620 REMARK 3 L13: 1.3719 L23: 1.9526 REMARK 3 S TENSOR REMARK 3 S11: 0.0666 S12: -0.2669 S13: 0.2429 REMARK 3 S21: -0.0858 S22: 0.2085 S23: -0.2501 REMARK 3 S31: -0.5725 S32: 0.4265 S33: -0.1400 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 20 THROUGH 23 OR REMARK 3 RESID 25 THROUGH 31 OR RESID 33 THROUGH REMARK 3 38 OR RESID 40 THROUGH 51 OR RESID 53 REMARK 3 THROUGH 60 OR RESID 62 THROUGH 64 OR REMARK 3 RESID 66 THROUGH 76 OR RESID 78 THROUGH REMARK 3 106 OR (RESID 107 AND (NAME N OR NAME CA REMARK 3 OR NAME C OR NAME O OR NAME CB )) OR REMARK 3 RESID 108 THROUGH 130 OR RESID 133 REMARK 3 THROUGH 145 OR RESID 147 THROUGH 155 OR REMARK 3 RESID 157 THROUGH 168 OR (RESID 169 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB )) OR RESID 170 THROUGH 171 OR REMARK 3 RESID 173 THROUGH 177 OR RESID 180 REMARK 3 THROUGH 188 OR RESID 190 OR RESID 192 REMARK 3 THROUGH 208 OR RESID 210 OR RESID 212 REMARK 3 THROUGH 229 OR RESID 231)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 20 THROUGH 23 OR REMARK 3 RESID 25 THROUGH 31 OR RESID 33 THROUGH REMARK 3 38 OR RESID 40 THROUGH 51 OR RESID 53 REMARK 3 THROUGH 60 OR RESID 62 THROUGH 64 OR REMARK 3 RESID 66 THROUGH 76 OR RESID 78 THROUGH REMARK 3 104 OR (RESID 105 AND (NAME N OR NAME CA REMARK 3 OR NAME C OR NAME O OR NAME CB )) OR REMARK 3 RESID 106 THROUGH 130 OR RESID 133 REMARK 3 THROUGH 145 OR RESID 147 THROUGH 155 OR REMARK 3 RESID 157 THROUGH 167 OR (RESID 168 REMARK 3 THROUGH 169 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB )) OR RESID REMARK 3 170 THROUGH 171 OR RESID 173 THROUGH 177 REMARK 3 OR RESID 180 THROUGH 188 OR RESID 190 OR REMARK 3 RESID 192 THROUGH 208 OR RESID 210 OR REMARK 3 RESID 212 THROUGH 229 OR RESID 231)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XQ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250544. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 33.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.190 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: 4LP4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M NAOAC (PH 7.5), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 68.27133 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 34.13567 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 0.00000 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 68.27133 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 34.13567 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 -102.18000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 -102.18000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -34.13567 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -34.13567 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 67 CG CD OE1 NE2 REMARK 470 ARG A 104 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 105 CG OD1 ND2 REMARK 470 LYS A 140 CG CD CE NZ REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 ARG A 203 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 218 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 67 CG CD OE1 NE2 REMARK 470 ARG B 104 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 LYS B 140 CG CD CE NZ REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 LYS B 169 CG CD CE NZ REMARK 470 ARG B 203 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 218 CG CD NE CZ NH1 NH2 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 OE2 GLU B 132 NH1 ARG B 228 1.57 REMARK 500 OE2 GLU A 32 O HOH A 401 1.88 REMARK 500 NH2 ARG A 178 O HOH A 402 2.11 REMARK 500 O HOH B 481 O HOH B 600 2.15 REMARK 500 O HOH A 477 O HOH A 594 2.18 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 NH1 ARG A 179 O GLY B 56 2454 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 179 NE - CZ - NH2 ANGL. DEV. = 3.6 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 60 -139.03 58.43 REMARK 500 PRO A 151 -177.97 -61.70 REMARK 500 ASP A 160 52.83 37.00 REMARK 500 ALA B 60 -141.89 58.94 REMARK 500 ALA B 60 -136.33 58.94 REMARK 500 PRO B 151 -178.38 -62.02 REMARK 500 ASP B 160 52.73 37.02 REMARK 500 LYS B 169 59.19 -155.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 629 DISTANCE = 6.37 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V74 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V74 B 305 DBREF 6XQ1 A 23 231 UNP Q15109 RAGE_HUMAN 23 231 DBREF 6XQ1 B 23 231 UNP Q15109 RAGE_HUMAN 23 231 SEQADV 6XQ1 GLY A 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ1 ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ1 MET A 22 UNP Q15109 EXPRESSION TAG SEQADV 6XQ1 GLY B 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ1 ALA B 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ1 MET B 22 UNP Q15109 EXPRESSION TAG SEQRES 1 A 212 GLY ALA MET ALA GLN ASN ILE THR ALA ARG ILE GLY GLU SEQRES 2 A 212 PRO LEU VAL LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO SEQRES 3 A 212 PRO GLN ARG LEU GLU TRP LYS LEU ASN THR GLY ARG THR SEQRES 4 A 212 GLU ALA TRP LYS VAL LEU SER PRO GLN GLY GLY GLY PRO SEQRES 5 A 212 TRP ASP SER VAL ALA ARG VAL LEU PRO ASN GLY SER LEU SEQRES 6 A 212 PHE LEU PRO ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE SEQRES 7 A 212 ARG CYS GLN ALA MET ASN ARG ASN GLY LYS GLU THR LYS SEQRES 8 A 212 SER ASN TYR ARG VAL ARG VAL TYR GLN ILE PRO GLY LYS SEQRES 9 A 212 PRO GLU ILE VAL ASP SER ALA SER GLU LEU THR ALA GLY SEQRES 10 A 212 VAL PRO ASN LYS VAL GLY THR CYS VAL SER GLU GLY SER SEQRES 11 A 212 TYR PRO ALA GLY THR LEU SER TRP HIS LEU ASP GLY LYS SEQRES 12 A 212 PRO LEU VAL PRO ASN GLU LYS GLY VAL SER VAL LYS GLU SEQRES 13 A 212 GLN THR ARG ARG HIS PRO GLU THR GLY LEU PHE THR LEU SEQRES 14 A 212 GLN SER GLU LEU MET VAL THR PRO ALA ARG GLY GLY ASP SEQRES 15 A 212 PRO ARG PRO THR PHE SER CYS SER PHE SER PRO GLY LEU SEQRES 16 A 212 PRO ARG HIS ARG ALA LEU ARG THR ALA PRO ILE GLN PRO SEQRES 17 A 212 ARG VAL TRP GLU SEQRES 1 B 212 GLY ALA MET ALA GLN ASN ILE THR ALA ARG ILE GLY GLU SEQRES 2 B 212 PRO LEU VAL LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO SEQRES 3 B 212 PRO GLN ARG LEU GLU TRP LYS LEU ASN THR GLY ARG THR SEQRES 4 B 212 GLU ALA TRP LYS VAL LEU SER PRO GLN GLY GLY GLY PRO SEQRES 5 B 212 TRP ASP SER VAL ALA ARG VAL LEU PRO ASN GLY SER LEU SEQRES 6 B 212 PHE LEU PRO ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE SEQRES 7 B 212 ARG CYS GLN ALA MET ASN ARG ASN GLY LYS GLU THR LYS SEQRES 8 B 212 SER ASN TYR ARG VAL ARG VAL TYR GLN ILE PRO GLY LYS SEQRES 9 B 212 PRO GLU ILE VAL ASP SER ALA SER GLU LEU THR ALA GLY SEQRES 10 B 212 VAL PRO ASN LYS VAL GLY THR CYS VAL SER GLU GLY SER SEQRES 11 B 212 TYR PRO ALA GLY THR LEU SER TRP HIS LEU ASP GLY LYS SEQRES 12 B 212 PRO LEU VAL PRO ASN GLU LYS GLY VAL SER VAL LYS GLU SEQRES 13 B 212 GLN THR ARG ARG HIS PRO GLU THR GLY LEU PHE THR LEU SEQRES 14 B 212 GLN SER GLU LEU MET VAL THR PRO ALA ARG GLY GLY ASP SEQRES 15 B 212 PRO ARG PRO THR PHE SER CYS SER PHE SER PRO GLY LEU SEQRES 16 B 212 PRO ARG HIS ARG ALA LEU ARG THR ALA PRO ILE GLN PRO SEQRES 17 B 212 ARG VAL TRP GLU HET ACT A 301 4 HET ACT A 302 4 HET ACT A 303 4 HET ACT A 304 4 HET CL A 305 1 HET V74 A 306 37 HET ACT B 301 4 HET ACT B 302 4 HET ACT B 303 4 HET CL B 304 1 HET V74 B 305 37 HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM V74 3-[3-({[3-(4-CARBOXYPHENOXY)PHENYL]METHOXY}METHYL) HETNAM 2 V74 PHENYL]-1H-INDOLE-2-CARBOXYLIC ACID FORMUL 3 ACT 7(C2 H3 O2 1-) FORMUL 7 CL 2(CL 1-) FORMUL 8 V74 2(C30 H23 N O6) FORMUL 14 HOH *461(H2 O) HELIX 1 AA1 GLY A 70 VAL A 75 5 6 HELIX 2 AA2 GLY A 90 ASP A 93 5 4 HELIX 3 AA3 GLY B 70 VAL B 75 5 6 HELIX 4 AA4 GLY B 90 ASP B 93 5 4 SHEET 1 AA1 5 GLN A 24 ARG A 29 0 SHEET 2 AA1 5 GLU A 108 TYR A 118 1 O ARG A 114 N ILE A 26 SHEET 3 AA1 5 GLY A 95 MET A 102 -1 N PHE A 97 O TYR A 113 SHEET 4 AA1 5 ARG A 48 THR A 55 -1 N LYS A 52 O ARG A 98 SHEET 5 AA1 5 LYS A 62 LEU A 64 -1 O LEU A 64 N TRP A 51 SHEET 1 AA2 3 LEU A 34 LEU A 36 0 SHEET 2 AA2 3 LEU A 84 LEU A 86 -1 O LEU A 84 N LEU A 36 SHEET 3 AA2 3 ARG A 77 VAL A 78 -1 N ARG A 77 O PHE A 85 SHEET 1 AA3 4 GLU A 125 VAL A 127 0 SHEET 2 AA3 4 ASN A 139 SER A 149 -1 O THR A 143 N VAL A 127 SHEET 3 AA3 4 PHE A 186 VAL A 194 -1 O SER A 190 N CYS A 144 SHEET 4 AA3 4 VAL A 171 ARG A 179 -1 N SER A 172 O MET A 193 SHEET 1 AA4 2 GLU A 132 THR A 134 0 SHEET 2 AA4 2 ARG A 228 TRP A 230 1 O TRP A 230 N LEU A 133 SHEET 1 AA5 4 LYS A 162 LEU A 164 0 SHEET 2 AA5 4 THR A 154 LEU A 159 -1 N TRP A 157 O LEU A 164 SHEET 3 AA5 4 PHE A 206 SER A 211 -1 O SER A 211 N THR A 154 SHEET 4 AA5 4 LEU A 220 ARG A 221 -1 O LEU A 220 N PHE A 210 SHEET 1 AA6 5 GLN B 24 ARG B 29 0 SHEET 2 AA6 5 GLU B 108 TYR B 118 1 O ARG B 114 N ILE B 26 SHEET 3 AA6 5 GLY B 95 MET B 102 -1 N PHE B 97 O TYR B 113 SHEET 4 AA6 5 LEU B 49 THR B 55 -1 N LYS B 52 O ARG B 98 SHEET 5 AA6 5 LYS B 62 LEU B 64 -1 O LEU B 64 N TRP B 51 SHEET 1 AA7 3 LEU B 34 LEU B 36 0 SHEET 2 AA7 3 LEU B 84 LEU B 86 -1 O LEU B 86 N LEU B 34 SHEET 3 AA7 3 ARG B 77 VAL B 78 -1 N ARG B 77 O PHE B 85 SHEET 1 AA8 4 GLU B 125 VAL B 127 0 SHEET 2 AA8 4 ASN B 139 SER B 149 -1 O THR B 143 N VAL B 127 SHEET 3 AA8 4 PHE B 186 VAL B 194 -1 O SER B 190 N CYS B 144 SHEET 4 AA8 4 VAL B 171 ARG B 179 -1 N SER B 172 O MET B 193 SHEET 1 AA9 2 GLU B 132 THR B 134 0 SHEET 2 AA9 2 ARG B 228 TRP B 230 1 O TRP B 230 N LEU B 133 SHEET 1 AB1 4 LYS B 162 PRO B 163 0 SHEET 2 AB1 4 THR B 154 LEU B 159 -1 N LEU B 159 O LYS B 162 SHEET 3 AB1 4 PHE B 206 SER B 211 -1 O SER B 211 N THR B 154 SHEET 4 AB1 4 LEU B 220 ARG B 221 -1 O LEU B 220 N PHE B 210 SSBOND 1 CYS A 38 CYS A 99 1555 1555 2.09 SSBOND 2 CYS A 144 CYS A 208 1555 1555 2.05 SSBOND 3 CYS B 38 CYS B 99 1555 1555 2.09 SSBOND 4 CYS B 144 CYS B 208 1555 1555 2.06 CISPEP 1 PRO A 45 PRO A 46 0 6.49 CISPEP 2 TYR A 150 PRO A 151 0 -13.11 CISPEP 3 PRO B 45 PRO B 46 0 6.28 CISPEP 4 TYR B 150 PRO B 151 0 -12.54 SITE 1 AC1 9 GLY A 20 ALA A 21 ALA A 23 ALA A 60 SITE 2 AC1 9 ILE A 96 ARG A 98 ASN A 112 HOH A 543 SITE 3 AC1 9 HOH A 579 SITE 1 AC2 6 LYS A 52 TRP A 61 ARG A 98 V74 A 306 SITE 2 AC2 6 HOH A 420 HOH A 543 SITE 1 AC3 7 GLN A 24 LYS A 39 SER A 111 ASN A 112 SITE 2 AC3 7 TYR A 113 HOH A 514 LYS B 174 SITE 1 AC4 7 GLU A 175 GLN A 176 THR A 177 HOH A 469 SITE 2 AC4 7 ARG B 116 HOH B 415 HOH B 532 SITE 1 AC5 3 GLU A 59 ARG B 178 ARG B 179 SITE 1 AC6 9 ARG A 48 LEU A 49 GLU A 50 LYS A 52 SITE 2 AC6 9 ARG A 98 GLN A 100 LYS A 110 SER A 111 SITE 3 AC6 9 ACT A 302 SITE 1 AC7 9 GLY B 20 ALA B 21 ALA B 23 ALA B 60 SITE 2 AC7 9 ILE B 96 ARG B 98 ASN B 112 HOH B 462 SITE 3 AC7 9 HOH B 505 SITE 1 AC8 6 LYS B 52 TRP B 61 ARG B 98 V74 B 305 SITE 2 AC8 6 HOH B 429 HOH B 505 SITE 1 AC9 6 LYS A 174 GLN B 24 LYS B 39 SER B 111 SITE 2 AC9 6 ASN B 112 TYR B 113 SITE 1 AD1 4 ARG A 178 ARG A 179 HOH A 430 GLU B 59 SITE 1 AD2 9 ARG B 48 LEU B 49 GLU B 50 LYS B 52 SITE 2 AD2 9 ARG B 98 GLN B 100 LYS B 110 SER B 111 SITE 3 AD2 9 ACT B 302 CRYST1 102.180 102.180 102.407 90.00 90.00 120.00 P 62 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 0.009787 0.005650 0.000000 0.00000 SCALE2 0.000000 0.011301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009765 0.00000