HEADER SIGNALING PROTEIN 09-JUL-20 6XQ8 TITLE RECEPTOR FOR ADVANCED GLYCATION END PRODUCTS VC1 DOMAIN IN COMPLEX TITLE 2 WITH FRAGMENTS 1 & 11 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 6XQ8 1 REMARK REVDAT 6 15-DEC-21 6XQ8 1 AUTHOR JRNL REVDAT 5 20-OCT-21 6XQ8 1 JRNL REVDAT 4 11-AUG-21 6XQ8 1 REMARK REVDAT 3 04-AUG-21 6XQ8 1 JRNL REVDAT 2 28-JUL-21 6XQ8 1 JRNL REVDAT 1 14-JUL-21 6XQ8 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. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 54335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2730 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 45.6900 - 4.9400 0.99 2607 168 0.2020 0.1894 REMARK 3 2 4.9400 - 3.9200 1.00 2581 151 0.1724 0.2183 REMARK 3 3 3.9200 - 3.4200 1.00 2595 136 0.1924 0.2123 REMARK 3 4 3.4200 - 3.1100 1.00 2625 104 0.2045 0.2887 REMARK 3 5 3.1100 - 2.8900 1.00 2591 121 0.2250 0.2281 REMARK 3 6 2.8900 - 2.7200 1.00 2585 144 0.2233 0.2348 REMARK 3 7 2.7200 - 2.5800 1.00 2593 121 0.2141 0.2117 REMARK 3 8 2.5800 - 2.4700 1.00 2582 140 0.2066 0.2324 REMARK 3 9 2.4700 - 2.3700 1.00 2574 119 0.2094 0.2098 REMARK 3 10 2.3700 - 2.2900 1.00 2565 159 0.2038 0.2386 REMARK 3 11 2.2900 - 2.2200 1.00 2577 132 0.1926 0.2287 REMARK 3 12 2.2200 - 2.1600 1.00 2573 134 0.1858 0.1940 REMARK 3 13 2.1600 - 2.1000 1.00 2574 158 0.1825 0.2058 REMARK 3 14 2.1000 - 2.0500 1.00 2553 156 0.1830 0.1784 REMARK 3 15 2.0500 - 2.0000 1.00 2548 146 0.1917 0.2231 REMARK 3 16 2.0000 - 1.9600 1.00 2600 103 0.1915 0.2040 REMARK 3 17 1.9600 - 1.9200 1.00 2558 159 0.1888 0.1985 REMARK 3 18 1.9200 - 1.8800 1.00 2585 116 0.2040 0.2473 REMARK 3 19 1.8800 - 1.8500 1.00 2588 135 0.2044 0.2166 REMARK 3 20 1.8500 - 1.8200 0.99 2551 128 0.2168 0.2280 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) : 0.143 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.91 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 : 0.020 3216 REMARK 3 ANGLE : 1.504 4403 REMARK 3 CHIRALITY : 0.109 477 REMARK 3 PLANARITY : 0.011 582 REMARK 3 DIHEDRAL : 19.140 1130 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 60 or REMARK 3 resid 62 through 145 or resid 147 through REMARK 3 231)) 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 60 or REMARK 3 resid 62 through 145 or resid 147 through REMARK 3 181 or (resid 182 and (name N or name CA REMARK 3 or name C or name O or name CB )) or REMARK 3 resid 183 through 212 or resid 220 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 6XQ8 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_1000250548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-16 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 : 107292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.050 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 (%): 63.14 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 68.51933 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 34.25967 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 68.51933 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 34.25967 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: 10750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 51.00850 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -88.34931 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 51.00850 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 -88.34931 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -34.25967 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 -34.25967 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 GLY A 213 REMARK 465 LEU A 214 REMARK 465 PRO A 215 REMARK 465 ARG A 216 REMARK 465 HIS A 217 REMARK 465 ARG A 218 REMARK 465 ALA A 219 REMARK 465 GLY B 213 REMARK 465 LEU B 214 REMARK 465 PRO B 215 REMARK 465 ARG B 216 REMARK 465 HIS B 217 REMARK 465 ARG B 218 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 ARG A 48 CG CD NE CZ NH1 NH2 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 GLU A 108 CG CD OE1 OE2 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 GLU A 182 CG CD OE1 OE2 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 221 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 ARG B 48 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 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 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 ARG B 198 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 203 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 221 CG CD NE CZ NH1 NH2 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 TRP A 230 CB TRP A 230 CG -0.329 REMARK 500 TRP A 230 CE2 TRP A 230 CZ2 -0.105 REMARK 500 TRP A 230 CE3 TRP A 230 CZ3 -0.119 REMARK 500 TRP B 230 CB TRP B 230 CG -0.325 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 TRP A 230 CB - CA - C ANGL. DEV. = -14.4 DEGREES REMARK 500 TRP B 230 CB - CA - C ANGL. DEV. = -16.0 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 60 -143.49 58.35 REMARK 500 PRO A 151 -177.26 -61.56 REMARK 500 LYS A 169 73.16 55.59 REMARK 500 ALA B 60 -142.62 58.82 REMARK 500 PRO B 151 -176.93 -62.15 REMARK 500 LYS B 169 71.44 45.77 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 TRP A 230 -10.09 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 B 490 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH B 491 DISTANCE = 8.67 ANGSTROMS REMARK 525 HOH B 492 DISTANCE = 11.45 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 V6M A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6P A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6P A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6M B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue V6P B 306 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 DBREF 6XQ8 A 23 231 UNP Q15109 RAGE_HUMAN 23 231 DBREF 6XQ8 B 23 231 UNP Q15109 RAGE_HUMAN 23 231 SEQADV 6XQ8 GLY A 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ8 ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ8 MET A 22 UNP Q15109 EXPRESSION TAG SEQADV 6XQ8 GLY B 20 UNP Q15109 EXPRESSION TAG SEQADV 6XQ8 ALA B 21 UNP Q15109 EXPRESSION TAG SEQADV 6XQ8 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 V6M A 305 19 HET V6P A 306 14 HET V6P A 307 14 HET ACT B 301 4 HET ACT B 302 4 HET CL B 303 1 HET CL B 304 1 HET V6M B 305 19 HET V6P B 306 14 HETNAM ACT ACETATE ION HETNAM V6M 7-METHYL-3-PHENYL-1H-INDOLE-2-CARBOXYLIC ACID HETNAM V6P 3-PHENOXYPHENOL HETNAM CL CHLORIDE ION FORMUL 3 ACT 6(C2 H3 O2 1-) FORMUL 7 V6M 2(C16 H13 N O2) FORMUL 8 V6P 3(C12 H10 O2) FORMUL 12 CL 2(CL 1-) FORMUL 16 HOH *176(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 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 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 3 LYS A 162 PRO A 163 0 SHEET 2 AA5 3 THR A 154 LEU A 159 -1 N LEU A 159 O LYS A 162 SHEET 3 AA5 3 PHE A 206 SER A 211 -1 O SER A 211 N THR A 154 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 SER B 129 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 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 3 LYS B 162 PRO B 163 0 SHEET 2 AB1 3 THR B 154 LEU B 159 -1 N LEU B 159 O LYS B 162 SHEET 3 AB1 3 PHE B 206 SER B 211 -1 O SER B 211 N THR B 154 SSBOND 1 CYS A 38 CYS A 99 1555 1555 2.12 SSBOND 2 CYS A 144 CYS A 208 1555 1555 2.05 SSBOND 3 CYS B 38 CYS B 99 1555 1555 2.11 SSBOND 4 CYS B 144 CYS B 208 1555 1555 2.05 CISPEP 1 PRO A 45 PRO A 46 0 4.19 CISPEP 2 TYR A 150 PRO A 151 0 -10.51 CISPEP 3 PRO B 45 PRO B 46 0 5.14 CISPEP 4 TYR B 150 PRO B 151 0 -9.45 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 404 SITE 3 AC1 9 HOH A 460 SITE 1 AC2 7 LYS A 52 TRP A 61 VAL A 63 ARG A 98 SITE 2 AC2 7 V6M A 305 HOH A 408 HOH A 460 SITE 1 AC3 5 LYS A 39 SER A 111 ASN A 112 TYR A 113 SITE 2 AC3 5 LYS B 174 SITE 1 AC4 5 LYS A 174 LYS B 39 SER B 111 ASN B 112 SITE 2 AC4 5 TYR B 113 SITE 1 AC5 10 GLU A 50 LYS A 52 ARG A 98 CYS A 99 SITE 2 AC5 10 GLN A 100 LYS A 110 SER A 111 ASN A 112 SITE 3 AC5 10 ACT A 302 HOH A 417 SITE 1 AC6 6 ARG A 48 LEU A 49 GLU A 50 SER A 65 SITE 2 AC6 6 PRO A 66 GLN A 100 SITE 1 AC7 7 ASP A 73 ARG A 77 PRO A 87 ASP B 73 SITE 2 AC7 7 ARG B 77 PHE B 85 PRO B 87 SITE 1 AC8 9 GLY B 20 ALA B 21 ALA B 23 ALA B 60 SITE 2 AC8 9 ILE B 96 ARG B 98 ASN B 112 HOH B 404 SITE 3 AC8 9 HOH B 470 SITE 1 AC9 7 LYS B 52 TRP B 61 VAL B 63 ARG B 98 SITE 2 AC9 7 V6M B 305 HOH B 463 HOH B 470 SITE 1 AD1 4 GLU A 59 HOH A 457 ARG B 178 ARG B 179 SITE 1 AD2 4 ARG A 178 ARG A 179 GLU B 59 HOH B 442 SITE 1 AD3 8 GLU B 50 LYS B 52 ARG B 98 CYS B 99 SITE 2 AD3 8 GLN B 100 LYS B 110 SER B 111 ACT B 302 SITE 1 AD4 6 ARG B 48 LEU B 49 GLU B 50 SER B 65 SITE 2 AD4 6 PRO B 66 GLN B 100 CRYST1 102.017 102.017 102.779 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 0.009802 0.005659 0.000000 0.00000 SCALE2 0.000000 0.011319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009730 0.00000