HEADER SIGNALING PROTEIN 09-JUL-20 6XQ3 TITLE RECEPTOR FOR ADVANCED GLYCATION END PRODUCTS VC1 DOMAIN IN COMPLEX TITLE 2 WITH 3-(3-(((3-(4-CARBOXYPHENOXY)BENZYL)OXY)METHYL)PHENYL)-1H-INDOLE- TITLE 3 2-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, IG-LIKE DOMAIN, RECEPTOR, ADVANCED GLYCATION END PRODUCTS, KEYWDS 2 SIGNALING 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 6XQ3 1 REMARK REVDAT 6 15-DEC-21 6XQ3 1 AUTHOR JRNL REVDAT 5 20-OCT-21 6XQ3 1 JRNL REVDAT 4 11-AUG-21 6XQ3 1 REMARK REVDAT 3 04-AUG-21 6XQ3 1 JRNL REVDAT 2 28-JUL-21 6XQ3 1 JRNL REVDAT 1 14-JUL-21 6XQ3 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. 1.71 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 64896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 3191 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 40.6800 - 4.8500 0.93 2588 121 0.1719 0.2236 REMARK 3 2 4.8500 - 3.8500 0.97 2659 142 0.1550 0.1544 REMARK 3 3 3.8500 - 3.3700 0.98 2687 120 0.1759 0.1780 REMARK 3 4 3.3700 - 3.0600 0.98 2682 134 0.2086 0.2150 REMARK 3 5 3.0600 - 2.8400 0.98 2628 171 0.2172 0.2677 REMARK 3 6 2.8400 - 2.6700 0.99 2721 125 0.2009 0.2101 REMARK 3 7 2.6700 - 2.5400 0.99 2634 177 0.2173 0.2520 REMARK 3 8 2.5400 - 2.4300 0.99 2711 124 0.2089 0.2595 REMARK 3 9 2.4300 - 2.3300 0.99 2693 135 0.2099 0.2662 REMARK 3 10 2.3300 - 2.2500 1.00 2709 136 0.2031 0.2642 REMARK 3 11 2.2500 - 2.1800 1.00 2708 138 0.2046 0.2516 REMARK 3 12 2.1800 - 2.1200 1.00 2718 144 0.1854 0.2082 REMARK 3 13 2.1200 - 2.0600 1.00 2716 116 0.1947 0.2018 REMARK 3 14 2.0600 - 2.0100 1.00 2711 150 0.2004 0.2493 REMARK 3 15 2.0100 - 1.9700 1.00 2713 132 0.2002 0.1981 REMARK 3 16 1.9700 - 1.9300 1.00 2697 132 0.1890 0.2107 REMARK 3 17 1.9300 - 1.8900 1.00 2727 150 0.1924 0.2129 REMARK 3 18 1.8900 - 1.8500 1.00 2701 136 0.1909 0.2052 REMARK 3 19 1.8500 - 1.8200 1.00 2692 164 0.2071 0.2513 REMARK 3 20 1.8200 - 1.7900 1.00 2712 135 0.1942 0.2745 REMARK 3 21 1.7900 - 1.7600 1.00 2695 146 0.2038 0.2521 REMARK 3 22 1.7600 - 1.7300 1.00 2728 133 0.2087 0.2706 REMARK 3 23 1.7300 - 1.7100 0.92 2475 130 0.2182 0.2605 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) : 0.177 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.38 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 : 0.018 3539 REMARK 3 ANGLE : 1.766 4865 REMARK 3 CHIRALITY : 0.108 505 REMARK 3 PLANARITY : 0.010 648 REMARK 3 DIHEDRAL : 21.656 514 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -30.7982 -17.7286 19.9232 REMARK 3 T TENSOR REMARK 3 T11: 0.2465 T22: 0.1760 REMARK 3 T33: 0.1941 T12: 0.0581 REMARK 3 T13: 0.0233 T23: -0.0429 REMARK 3 L TENSOR REMARK 3 L11: 0.1866 L22: 0.1310 REMARK 3 L33: 0.3731 L12: 0.0341 REMARK 3 L13: 0.1324 L23: -0.2522 REMARK 3 S TENSOR REMARK 3 S11: 0.0164 S12: -0.0233 S13: 0.0281 REMARK 3 S21: -0.0300 S22: 0.0416 S23: -0.0468 REMARK 3 S31: -0.0576 S32: 0.1086 S33: -0.0572 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 60 OR RESID 62 THROUGH REMARK 3 113 OR RESID 115 THROUGH 130 OR RESID 133 REMARK 3 THROUGH 145 OR RESID 147 THROUGH 171 OR REMARK 3 RESID 173 THROUGH 177 OR RESID 180 REMARK 3 THROUGH 188 OR RESID 190 THROUGH 208 OR REMARK 3 RESID 210 OR RESID 212 THROUGH 231)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 20 THROUGH 23 OR REMARK 3 RESID 25 THROUGH 60 OR RESID 62 THROUGH REMARK 3 66 OR (RESID 67 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB )) OR RESID REMARK 3 68 THROUGH 106 OR (RESID 107 AND (NAME N REMARK 3 OR NAME CA OR NAME C OR NAME O OR NAME CB REMARK 3 )) OR RESID 108 THROUGH 113 OR RESID 115 REMARK 3 THROUGH 122 OR (RESID 123 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 124 THROUGH 130 OR RESID 133 REMARK 3 THROUGH 145 OR RESID 147 THROUGH 171 OR REMARK 3 RESID 173 THROUGH 177 OR RESID 180 REMARK 3 THROUGH 188 OR RESID 190 THROUGH 208 OR REMARK 3 RESID 210 OR RESID 212 THROUGH 220 OR REMARK 3 (RESID 221 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 222 REMARK 3 THROUGH 231)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XQ3 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_1000250545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 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 : 66015 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.890 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 67.87467 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 33.93733 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 67.87467 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 33.93733 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: 11070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 -102.47500 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 -102.47500 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -33.93733 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 -33.93733 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 LYS A 44 CG CD CE NZ 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 107 CG CD CE NZ REMARK 470 LYS A 123 CG CD CE NZ 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 LYS A 169 CG CD CE NZ REMARK 470 ARG A 203 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 218 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 221 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 ARG B 104 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 105 CG OD1 ND2 REMARK 470 LYS B 140 CG CD CE NZ REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 GLU B 168 CG CD OE1 OE2 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 OXT ACT A 303 O HOH A 401 1.98 REMARK 500 NZ LYS B 110 O17 V6Y B 303 2.03 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 HOH B 508 2454 2.11 REMARK 500 NH2 ARG B 179 O HOH A 511 3445 2.13 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 LYS A 43 CD - CE - NZ ANGL. DEV. = -28.7 DEGREES REMARK 500 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 114 NE - CZ - NH1 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 -139.26 57.05 REMARK 500 PRO A 151 -177.15 -63.24 REMARK 500 ARG A 216 -4.95 72.91 REMARK 500 ALA B 60 -140.22 57.55 REMARK 500 PRO B 151 -176.97 -62.86 REMARK 500 ARG B 216 -3.17 71.88 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 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 CL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6Y A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6Y 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 CL B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6Y B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6Y B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XQ1 RELATED DB: PDB REMARK 900 RAGE VC1 WITH A DIFFERENT COMPOUND DBREF 6XQ3 A 23 231 UNP Q15109 RAGE_HUMAN 23 231 DBREF 6XQ3 B 23 231 UNP Q15109 RAGE_HUMAN 23 231 SEQADV 6XQ3 GLY A 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ3 ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ3 MET A 22 UNP Q15109 EXPRESSION TAG SEQADV 6XQ3 GLY B 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ3 ALA B 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ3 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 CL A 304 1 HET V6Y A 305 36 HET V6Y A 306 36 HET ACT B 301 4 HET CL B 302 1 HET V6Y B 303 36 HET V6Y B 304 36 HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM V6Y 3-(3-{[3-(4-CARBOXYPHENOXY)PHENYL]METHOXY}PHENYL)-1H- HETNAM 2 V6Y INDOLE-2-CARBOXYLIC ACID FORMUL 3 ACT 4(C2 H3 O2 1-) FORMUL 6 CL 2(CL 1-) FORMUL 7 V6Y 4(C29 H21 N O6) FORMUL 13 HOH *256(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 GLY A 95 O VAL A 115 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 86 N LEU A 34 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 ARG A 228 N LEU A 133 SHEET 1 AA5 4 LYS A 162 PRO A 163 0 SHEET 2 AA5 4 THR A 154 LEU A 159 -1 N LEU A 159 O LYS A 162 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 ARG B 48 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 ARG B 178 O THR B 187 SHEET 1 AA9 2 GLU B 132 THR B 134 0 SHEET 2 AA9 2 ARG B 228 TRP B 230 1 O ARG B 228 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 2.14 SSBOND 2 CYS A 144 CYS A 208 1555 1555 2.06 SSBOND 3 CYS B 38 CYS B 99 1555 1555 2.13 SSBOND 4 CYS B 144 CYS B 208 1555 1555 2.04 CISPEP 1 PRO A 45 PRO A 46 0 5.29 CISPEP 2 TYR A 150 PRO A 151 0 -11.92 CISPEP 3 PRO B 45 PRO B 46 0 5.57 CISPEP 4 TYR B 150 PRO B 151 0 -11.85 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 407 SITE 3 AC1 9 HOH A 467 SITE 1 AC2 6 LYS A 52 TRP A 61 VAL A 63 ARG A 98 SITE 2 AC2 6 HOH A 415 HOH A 467 SITE 1 AC3 6 GLU A 175 THR A 177 HOH A 401 HOH A 476 SITE 2 AC3 6 ARG B 116 HOH B 409 SITE 1 AC4 4 GLU A 59 HOH A 493 ARG B 178 ARG B 179 SITE 1 AC5 12 ALA A 21 MET A 22 LYS A 39 GLU A 50 SITE 2 AC5 12 LYS A 52 ARG A 98 CYS A 99 GLN A 100 SITE 3 AC5 12 LYS A 110 SER A 111 ASN A 112 LYS B 174 SITE 1 AC6 11 PRO A 45 PRO A 66 GLN A 67 ASP A 73 SITE 2 AC6 11 SER A 74 ARG A 77 VAL A 78 LEU A 79 SITE 3 AC6 11 PRO A 80 PHE A 85 V6Y B 304 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 405 SITE 3 AC7 9 HOH B 473 SITE 1 AC8 4 ARG A 178 ARG A 179 GLU B 59 HOH B 451 SITE 1 AC9 12 LYS A 174 ALA B 21 MET B 22 LYS B 39 SITE 2 AC9 12 GLU B 50 LYS B 52 ARG B 98 CYS B 99 SITE 3 AC9 12 GLN B 100 LYS B 110 SER B 111 ASN B 112 SITE 1 AD1 12 SER A 74 PRO A 80 PRO A 87 V6Y A 306 SITE 2 AD1 12 ASP B 73 SER B 74 ARG B 77 VAL B 78 SITE 3 AD1 12 PRO B 80 PHE B 85 PRO B 87 HOH B 479 CRYST1 102.475 102.475 101.812 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 0.009758 0.005634 0.000000 0.00000 SCALE2 0.000000 0.011268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009822 0.00000