HEADER SIGNALING PROTEIN 09-JUL-20 6XQ9 TITLE RECEPTOR FOR ADVANCED GLYCATION END PRODUCTS VC1 DOMAIN IN COMPLEX TITLE 2 WITH FRAGMENTS 1 & 13 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 6XQ9 1 REMARK REVDAT 6 15-DEC-21 6XQ9 1 AUTHOR JRNL REVDAT 5 20-OCT-21 6XQ9 1 JRNL REVDAT 4 11-AUG-21 6XQ9 1 REMARK REVDAT 3 04-AUG-21 6XQ9 1 JRNL REVDAT 2 28-JUL-21 6XQ9 1 JRNL REVDAT 1 14-JUL-21 6XQ9 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. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 26834 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1388 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 34.0600 - 4.9500 0.99 2576 136 0.1947 0.2068 REMARK 3 2 4.9500 - 3.9300 1.00 2568 117 0.1721 0.1885 REMARK 3 3 3.9300 - 3.4400 1.00 2540 157 0.1914 0.2451 REMARK 3 4 3.4400 - 3.1200 1.00 2546 155 0.2222 0.2046 REMARK 3 5 3.1200 - 2.9000 1.00 2532 152 0.2419 0.2594 REMARK 3 6 2.9000 - 2.7300 1.00 2523 147 0.2624 0.2620 REMARK 3 7 2.7300 - 2.5900 1.00 2580 114 0.2462 0.3051 REMARK 3 8 2.5900 - 2.4800 1.00 2545 138 0.2520 0.2804 REMARK 3 9 2.4800 - 2.3800 1.00 2544 130 0.2566 0.3433 REMARK 3 10 2.3800 - 2.3000 0.98 2492 142 0.2696 0.3412 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) : 0.293 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.677 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.90 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 : 0.009 3282 REMARK 3 ANGLE : 1.327 4500 REMARK 3 CHIRALITY : 0.075 489 REMARK 3 PLANARITY : 0.010 597 REMARK 3 DIHEDRAL : 18.872 1146 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 20 through 107 or REMARK 3 (resid 108 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 109 REMARK 3 through 127 or (resid 128 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 129 through 130 or resid 132 REMARK 3 through 155 or resid 157 through 174 or REMARK 3 (resid 175 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 176 REMARK 3 through 208 or resid 210 through 213 or REMARK 3 (resid 214 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 215 REMARK 3 through 231)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 20 through 42 or REMARK 3 (resid 43 through 44 and (name N or name REMARK 3 CA or name C or name O or name CB )) or REMARK 3 resid 45 through 66 or (resid 67 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 68 through 130 or REMARK 3 resid 132 through 155 or resid 157 REMARK 3 through 208 or resid 210 through 225 or REMARK 3 (resid 226 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 227 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 6XQ9 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_1000250551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-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 : 52826 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 18.38 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4LP4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 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 68.11933 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 34.05967 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 68.11933 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 34.05967 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 43 CG CD CE NZ REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 GLN A 67 CG CD OE1 NE2 REMARK 470 GLN A 100 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 ASN A 167 CG OD1 ND2 REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 203 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 217 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 218 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 221 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 226 CG CD OE1 NE2 REMARK 470 GLU A 231 CG CD OE1 OE2 REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 GLN B 100 CG CD OE1 NE2 REMARK 470 ARG B 104 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 105 CG OD1 ND2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 LYS B 123 CG CD CE NZ REMARK 470 ASP B 128 CG OD1 OD2 REMARK 470 LYS B 140 CG CD CE NZ REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 ASN B 167 CG OD1 ND2 REMARK 470 GLU B 168 CG CD OE1 OE2 REMARK 470 LYS B 169 CG CD CE NZ REMARK 470 GLU B 175 CG CD OE1 OE2 REMARK 470 ARG B 198 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 203 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 214 CG CD1 CD2 REMARK 470 ARG B 216 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 217 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 218 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 221 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 231 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 37 CB LYS A 37 CG -0.173 REMARK 500 LYS A 37 CG LYS A 37 CD -0.207 REMARK 500 GLU A 94 CG GLU A 94 CD 0.094 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 GLU A 32 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LYS A 37 CB - CG - CD ANGL. DEV. = 17.4 DEGREES REMARK 500 LYS A 37 CD - CE - NZ ANGL. DEV. = 23.4 DEGREES REMARK 500 GLU A 94 CB - CA - C ANGL. DEV. = 15.4 DEGREES REMARK 500 GLU A 94 CG - CD - OE1 ANGL. DEV. = -16.2 DEGREES REMARK 500 GLN B 92 CA - CB - CG ANGL. DEV. = 20.4 DEGREES REMARK 500 GLN B 92 CB - CG - CD ANGL. DEV. = -16.5 DEGREES REMARK 500 MET B 102 CG - SD - CE ANGL. DEV. = 9.9 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 -136.09 60.87 REMARK 500 ASP A 128 99.51 46.37 REMARK 500 PRO A 151 179.98 -59.14 REMARK 500 ASN A 167 -30.40 61.32 REMARK 500 ALA B 60 -136.94 60.92 REMARK 500 GLN B 92 40.27 -90.85 REMARK 500 ASP B 128 88.29 39.60 REMARK 500 GLU B 168 116.98 -178.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 94 0.14 SIDE CHAIN REMARK 500 GLN B 92 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN B 92 -11.77 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 449 DISTANCE = 54.60 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 V6S A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6S A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6M A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6S B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6S B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6M B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XQ1 RELATED DB: PDB REMARK 900 RAGE VC1 WITH DIFFERENT LIGAND REMARK 900 RELATED ID: 6XQ3 RELATED DB: PDB REMARK 900 RAGE VC1 WITH DIFFERENT LIGAND REMARK 900 RELATED ID: 6XQ5 RELATED DB: PDB REMARK 900 RAGE VC1 WITH DIFFERENT LIGAND REMARK 900 RELATED ID: 6XQ6 RELATED DB: PDB REMARK 900 RAGE VC1 WITH DIFFERENT LIGAND REMARK 900 RELATED ID: 6XQ7 RELATED DB: PDB REMARK 900 RAGE VC1 WITH DIFFERENT LIGAND REMARK 900 RELATED ID: 6XQ8 RELATED DB: PDB REMARK 900 RAGE VC1 WITH DIFFERENT LIGAND DBREF 6XQ9 A 23 231 UNP Q15109 RAGE_HUMAN 23 231 DBREF 6XQ9 B 23 231 UNP Q15109 RAGE_HUMAN 23 231 SEQADV 6XQ9 GLY A 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ9 ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ9 MET A 22 UNP Q15109 EXPRESSION TAG SEQADV 6XQ9 GLY B 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ9 ALA B 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ9 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 V6S A 303 17 HET V6S A 304 17 HET V6M A 305 19 HET ACT B 301 4 HET ACT B 302 4 HET V6S B 303 17 HET V6S B 304 17 HET V6M B 305 19 HETNAM ACT ACETATE ION HETNAM V6S 4-(3-HYDROXYPHENOXY)BENZOIC ACID HETNAM V6M 7-METHYL-3-PHENYL-1H-INDOLE-2-CARBOXYLIC ACID FORMUL 3 ACT 4(C2 H3 O2 1-) FORMUL 5 V6S 4(C13 H10 O4) FORMUL 7 V6M 2(C16 H13 N O2) FORMUL 13 HOH *95(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 ALA A 101 O THR A 109 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 SER A 129 0 SHEET 2 AA3 4 ASN A 139 SER A 149 -1 O VAL A 145 N GLU A 125 SHEET 3 AA3 4 PHE A 186 VAL A 194 -1 O PHE A 186 N SER A 149 SHEET 4 AA3 4 VAL A 171 ARG A 179 -1 N ARG A 178 O THR A 187 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 116 N ILE B 26 SHEET 3 AA6 5 GLY B 95 MET B 102 -1 N ALA B 101 O THR B 109 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 VAL B 145 N GLU B 125 SHEET 3 AA8 4 PHE B 186 VAL B 194 -1 O PHE B 186 N SER B 149 SHEET 4 AA8 4 VAL B 171 ARG B 179 -1 N LYS B 174 O GLU B 191 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 2.05 SSBOND 2 CYS A 144 CYS A 208 1555 1555 2.02 SSBOND 3 CYS B 38 CYS B 99 1555 1555 2.04 SSBOND 4 CYS B 144 CYS B 208 1555 1555 2.03 CISPEP 1 PRO A 45 PRO A 46 0 6.28 CISPEP 2 TYR A 150 PRO A 151 0 -18.90 CISPEP 3 PRO B 45 PRO B 46 0 6.05 CISPEP 4 TYR B 150 PRO B 151 0 -19.36 SITE 1 AC1 8 GLY A 20 ALA A 21 ALA A 23 ALA A 60 SITE 2 AC1 8 ILE A 96 ARG A 98 ASN A 112 HOH A 430 SITE 1 AC2 6 ALA A 21 LYS A 52 TRP A 61 ARG A 98 SITE 2 AC2 6 V6M A 305 HOH A 430 SITE 1 AC3 6 ARG A 48 LEU A 49 GLU A 50 GLN A 100 SITE 2 AC3 6 ALA A 101 MET A 102 SITE 1 AC4 8 ASP A 73 SER A 74 ARG A 77 VAL A 78 SITE 2 AC4 8 PHE A 85 HOH A 418 HOH A 421 V6S B 303 SITE 1 AC5 9 ALA A 21 GLU A 50 LYS A 52 ARG A 98 SITE 2 AC5 9 GLN A 100 LYS A 110 SER A 111 ASN A 112 SITE 3 AC5 9 ACT A 302 SITE 1 AC6 8 HOH A 449 GLY B 20 ALA B 21 ALA B 23 SITE 2 AC6 8 ALA B 60 ILE B 96 ARG B 98 ASN B 112 SITE 1 AC7 6 HOH A 449 ALA B 21 LYS B 52 TRP B 61 SITE 2 AC7 6 VAL B 63 ARG B 98 SITE 1 AC8 9 PRO A 87 V6S A 304 ASP B 73 ALA B 76 SITE 2 AC8 9 ARG B 77 LEU B 79 PRO B 80 PHE B 85 SITE 3 AC8 9 PRO B 87 SITE 1 AC9 4 LEU B 49 GLU B 50 GLN B 100 MET B 102 SITE 1 AD1 8 ALA B 21 GLU B 50 LYS B 52 ARG B 98 SITE 2 AD1 8 GLN B 100 LYS B 110 SER B 111 ASN B 112 CRYST1 102.112 102.112 102.179 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 0.009793 0.005654 0.000000 0.00000 SCALE2 0.000000 0.011308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009787 0.00000 MTRIX1 1 0.502027 -0.864852 0.000584 -0.02546 1 MTRIX2 1 -0.864849 -0.502026 -0.002415 -0.16759 1 MTRIX3 1 0.002382 0.000707 -0.999997 -28.44311 1