HEADER SIGNALING PROTEIN 06-FEB-21 7LMW 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 6 18-OCT-23 7LMW 1 REMARK REVDAT 5 15-DEC-21 7LMW 1 JRNL REVDAT 4 20-OCT-21 7LMW 1 JRNL REVDAT 3 11-AUG-21 7LMW 1 REMARK REVDAT 2 04-AUG-21 7LMW 1 JRNL REVDAT 1 28-JUL-21 7LMW 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. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 20999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1084 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 33.4100 - 4.9900 0.99 2525 130 0.1902 0.2240 REMARK 3 2 4.9800 - 3.9600 1.00 2515 132 0.1679 0.2331 REMARK 3 3 3.9600 - 3.4600 0.99 2453 150 0.1807 0.2239 REMARK 3 4 3.4600 - 3.1400 1.00 2508 121 0.2203 0.2882 REMARK 3 5 3.1400 - 2.9200 1.00 2472 138 0.2244 0.2844 REMARK 3 6 2.9200 - 2.7500 1.00 2492 132 0.2642 0.3502 REMARK 3 7 2.7500 - 2.6100 1.00 2475 146 0.2128 0.2948 REMARK 3 8 2.6100 - 2.5000 1.00 2475 135 0.2475 0.2836 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) : 26.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.62 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 : 0.012 3181 REMARK 3 ANGLE : 1.411 4372 REMARK 3 CHIRALITY : 0.070 478 REMARK 3 PLANARITY : 0.010 577 REMARK 3 DIHEDRAL : 11.566 449 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): -30.7033 -17.7833 19.8555 REMARK 3 T TENSOR REMARK 3 T11: 0.2471 T22: 0.2131 REMARK 3 T33: 0.3417 T12: 0.0272 REMARK 3 T13: 0.0270 T23: -0.0610 REMARK 3 L TENSOR REMARK 3 L11: 0.2623 L22: 0.3889 REMARK 3 L33: 1.1345 L12: -0.1314 REMARK 3 L13: 0.1591 L23: -0.3626 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: -0.0301 S13: 0.0414 REMARK 3 S21: -0.0107 S22: 0.0429 S23: -0.0784 REMARK 3 S31: -0.1180 S32: 0.2087 S33: -0.0563 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 51 or REMARK 3 (resid 52 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 53 REMARK 3 through 212 or (resid 217 through 219 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 220 through 227 or REMARK 3 (resid 228 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 229 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 36 or REMARK 3 (resid 37 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 38 REMARK 3 through 91 or (resid 92 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 93 through 99 or (resid 100 REMARK 3 through 102 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 103 through 231)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7LMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-19 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0781 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20999 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 62.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 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 68.20400 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 34.10200 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 68.20400 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 34.10200 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLY B 213 REMARK 465 LEU B 214 REMARK 465 PRO B 215 REMARK 465 ARG B 216 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 37 CG CD CE NZ REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 44 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 GLN A 92 CG CD OE1 NE2 REMARK 470 GLN A 100 CG CD OE1 NE2 REMARK 470 MET A 102 CG SD CE 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 ASP A 128 CG OD1 OD2 REMARK 470 LYS A 140 CG CD CE NZ REMARK 470 ASP A 160 CG OD1 OD2 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 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 43 CG CD CE NZ REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 ARG B 48 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 52 CG CD CE NZ REMARK 470 GLN B 67 CG CD OE1 NE2 REMARK 470 MET B 102 CG SD CE 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 ASP B 160 CG OD1 OD2 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 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 GLN B 226 CG CD OE1 NE2 REMARK 470 ARG B 228 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: 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 NH2 ARG A 77 O16 Y6P B 501 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 OE2 GLU A 175 ND2 ASN B 25 5554 1.87 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. = -17.8 DEGREES REMARK 500 TRP A 230 N - CA - CB ANGL. DEV. = 21.5 DEGREES REMARK 500 TRP A 230 CA - CB - CG ANGL. DEV. = 16.2 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 -140.79 58.53 REMARK 500 VAL A 75 -52.07 -123.66 REMARK 500 GLU A 168 -121.52 -150.24 REMARK 500 ALA B 60 -142.69 59.97 REMARK 500 VAL B 75 -51.92 -124.44 REMARK 500 PRO B 151 178.16 -59.57 REMARK 500 GLU B 168 -123.55 -150.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 229 TRP A 230 139.77 REMARK 500 TRP A 230 GLU A 231 137.23 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 -10.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XQ1 RELATED DB: PDB REMARK 900 RELATED ID: 6XQ3 RELATED DB: PDB REMARK 900 RELATED ID: 6XQ5 RELATED DB: PDB REMARK 900 RELATED ID: 6XQ6 RELATED DB: PDB REMARK 900 RELATED ID: 6XQ7 RELATED DB: PDB REMARK 900 RELATED ID: 6XQ8 RELATED DB: PDB REMARK 900 RELATED ID: 6XQ9 RELATED DB: PDB REMARK 900 RELATED ID: 7LML RELATED DB: PDB DBREF 7LMW A 23 231 UNP Q15109 RAGE_HUMAN 23 231 DBREF 7LMW B 23 231 UNP Q15109 RAGE_HUMAN 23 231 SEQADV 7LMW GLY A 20 UNP Q15109 EXPRESSION TAG SEQADV 7LMW ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 7LMW MET A 22 UNP Q15109 EXPRESSION TAG SEQADV 7LMW GLY B 20 UNP Q15109 EXPRESSION TAG SEQADV 7LMW ALA B 21 UNP Q15109 EXPRESSION TAG SEQADV 7LMW 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 Y6P A 401 18 HET Y6P A 402 18 HET ACT A 403 4 HET ACT A 404 4 HET Y6P B 501 18 HET Y6P B 502 18 HET Y6P B 503 18 HET Y6P B 504 18 HET CL B 505 1 HET ACT B 506 4 HET ACT B 507 4 HET ACT B 508 4 HETNAM Y6P 7-METHYL-3-(1~{H}-PYRAZOL-4-YL)-1~{H}-INDOLE-2- HETNAM 2 Y6P CARBOXYLIC ACID HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION FORMUL 3 Y6P 6(C13 H11 N3 O2) FORMUL 5 ACT 5(C2 H3 O2 1-) FORMUL 11 CL CL 1- FORMUL 15 HOH *40(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 ASN A 112 N GLN A 24 SHEET 3 AA1 5 GLY A 95 MET A 102 -1 N ALA A 101 O THR A 109 SHEET 4 AA1 5 LEU A 49 THR A 55 -1 N LYS A 52 O ARG A 98 SHEET 5 AA1 5 LYS A 62 LEU A 64 -1 O LYS A 62 N LEU A 53 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 PHE A 186 N SER A 149 SHEET 4 AA3 4 SER A 172 ARG A 179 -1 N LYS A 174 O GLU A 191 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 LEU A 164 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 207 N HIS A 158 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 ASN B 112 N GLN B 24 SHEET 3 AA6 5 GLY B 95 MET B 102 -1 N CYS B 99 O SER B 111 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 LYS B 62 N LEU B 53 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 VAL B 194 N ASN B 139 SHEET 4 AA8 4 SER B 172 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 ARG B 228 N LEU B 133 SHEET 1 AB1 4 LYS B 162 LEU B 164 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 209 N SER B 156 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 2.03 SSBOND 2 CYS A 144 CYS A 208 1555 1555 2.02 SSBOND 3 CYS B 38 CYS B 99 1555 1555 2.03 SSBOND 4 CYS B 144 CYS B 208 1555 1555 2.03 CISPEP 1 PRO A 45 PRO A 46 0 7.00 CISPEP 2 TYR A 150 PRO A 151 0 -15.43 CISPEP 3 PRO B 45 PRO B 46 0 8.16 CISPEP 4 TYR B 150 PRO B 151 0 -15.96 CRYST1 101.885 101.885 102.306 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 0.009815 0.005667 0.000000 0.00000 SCALE2 0.000000 0.011333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009775 0.00000 MTRIX1 1 0.499801 0.866140 0.000502 -0.01135 1 MTRIX2 1 0.866140 -0.499801 -0.001109 0.04373 1 MTRIX3 1 -0.000709 0.000989 -0.999999 39.91769 1