HEADER TRANSPORT PROTEIN 13-FEB-10 3LSW TITLE ANIRACETAM BOUND TO THE LIGAND BINDING DOMAIN OF GLUA3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUA2 S1S2 DOMAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS, MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: RAT, MOUSE; SOURCE 4 ORGANISM_TAXID: 10116, 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ORIGAMI B (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-22B(+) KEYWDS GLUTAMATE RECEPTOR, GLUR3, GLUA3, AMPA RECEPTOR, NEUROTRANSMITTER KEYWDS 2 RECEPTOR, S1S2, ALLOSTERIC MODULATOR, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.H.AHMED,R.E.OSWALD REVDAT 3 06-SEP-23 3LSW 1 REMARK SEQADV HETSYN LINK REVDAT 2 02-AUG-17 3LSW 1 SOURCE REVDAT 1 16-MAR-10 3LSW 0 JRNL AUTH A.H.AHMED,R.E.OSWALD JRNL TITL PIRACETAM DEFINES A NEW BINDING SITE FOR ALLOSTERIC JRNL TITL 2 MODULATORS OF JRNL TITL 3 ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLE-PROPIONIC ACID JRNL TITL 4 (AMPA) RECEPTORS. JRNL REF J.MED.CHEM. V. 53 2197 2010 JRNL REFN ISSN 0022-2623 JRNL PMID 20163115 JRNL DOI 10.1021/JM901905J REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 30548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.340 REMARK 3 FREE R VALUE TEST SET COUNT : 1938 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 23.7337 - 4.2163 0.97 2236 152 0.1981 0.2148 REMARK 3 2 4.2163 - 3.3496 1.00 2164 151 0.1615 0.1820 REMARK 3 3 3.3496 - 2.9271 1.00 2141 146 0.1711 0.2516 REMARK 3 4 2.9271 - 2.6598 1.00 2122 147 0.1789 0.2136 REMARK 3 5 2.6598 - 2.4694 0.99 2103 141 0.1790 0.1929 REMARK 3 6 2.4694 - 2.3239 0.99 2100 146 0.1784 0.2181 REMARK 3 7 2.3239 - 2.2076 0.99 2067 139 0.1700 0.2290 REMARK 3 8 2.2076 - 2.1116 0.98 2063 136 0.1673 0.2124 REMARK 3 9 2.1116 - 2.0304 0.98 2063 132 0.1676 0.1947 REMARK 3 10 2.0304 - 1.9603 0.97 2010 132 0.1721 0.2220 REMARK 3 11 1.9603 - 1.8991 0.95 1993 131 0.1837 0.2522 REMARK 3 12 1.8991 - 1.8448 0.94 1965 139 0.1686 0.2236 REMARK 3 13 1.8448 - 1.7962 0.90 1881 130 0.1720 0.2154 REMARK 3 14 1.7962 - 1.7520 0.83 1702 116 0.1819 0.2477 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 : 0.39 REMARK 3 B_SOL : 59.32 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 2.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52490 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -6.34650 REMARK 3 B13 (A**2) : 3.24280 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.017 2098 REMARK 3 ANGLE : 1.655 2823 REMARK 3 CHIRALITY : 0.117 309 REMARK 3 PLANARITY : 0.010 353 REMARK 3 DIHEDRAL : 16.084 781 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3LSW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057688. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : RH COATED SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30548 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 43.0560 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.29800 REMARK 200 R SYM FOR SHELL (I) : 0.29800 REMARK 200 FOR SHELL : 4.190 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: PDB ENTRY 3DP6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-18% PEG8K, 0.1 M NA CACODYLATE, 0.1 REMARK 280 -0.15 M ZINC ACETATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.70450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.70450 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 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 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 68.70450 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 GLU A 67 -74.71 -76.32 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 GLU A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4MP A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LSF RELATED DB: PDB REMARK 900 RELATED ID: 3LSL RELATED DB: PDB REMARK 900 RELATED ID: 3LSX RELATED DB: PDB DBREF 3LSW A 4 117 UNP P19492 GRIA3_RAT 417 530 DBREF 3LSW A 120 261 UNP Q9Z2W9 GRIA3_MOUSE 658 799 SEQADV 3LSW GLY A 118 UNP P19492 LINKER SEQADV 3LSW THR A 119 UNP P19492 LINKER SEQRES 1 A 258 ARG THR ILE VAL VAL THR THR ILE LEU GLU SER PRO TYR SEQRES 2 A 258 VAL MET TYR LYS LYS ASN HIS GLU GLN LEU GLU GLY ASN SEQRES 3 A 258 GLU ARG TYR GLU GLY TYR CYS VAL ASP LEU ALA TYR GLU SEQRES 4 A 258 ILE ALA LYS HIS VAL ARG ILE LYS TYR LYS LEU SER ILE SEQRES 5 A 258 VAL GLY ASP GLY LYS TYR GLY ALA ARG ASP PRO GLU THR SEQRES 6 A 258 LYS ILE TRP ASN GLY MET VAL GLY GLU LEU VAL TYR GLY SEQRES 7 A 258 ARG ALA ASP ILE ALA VAL ALA PRO LEU THR ILE THR LEU SEQRES 8 A 258 VAL ARG GLU GLU VAL ILE ASP PHE SER LYS PRO PHE MET SEQRES 9 A 258 SER LEU GLY ILE SER ILE MET ILE LYS LYS GLY THR PRO SEQRES 10 A 258 ILE GLU SER ALA GLU ASP LEU ALA LYS GLN THR GLU ILE SEQRES 11 A 258 ALA TYR GLY THR LEU ASP SER GLY SER THR LYS GLU PHE SEQRES 12 A 258 PHE ARG ARG SER LYS ILE ALA VAL TYR GLU LYS MET TRP SEQRES 13 A 258 SER TYR MET LYS SER ALA GLU PRO SER VAL PHE THR LYS SEQRES 14 A 258 THR THR ALA ASP GLY VAL ALA ARG VAL ARG LYS SER LYS SEQRES 15 A 258 GLY LYS PHE ALA PHE LEU LEU GLU SER THR MET ASN GLU SEQRES 16 A 258 TYR ILE GLU GLN ARG LYS PRO CYS ASP THR MET LYS VAL SEQRES 17 A 258 GLY GLY ASN LEU ASP SER LYS GLY TYR GLY VAL ALA THR SEQRES 18 A 258 PRO LYS GLY SER ALA LEU GLY THR PRO VAL ASN LEU ALA SEQRES 19 A 258 VAL LEU LYS LEU SER GLU GLN GLY ILE LEU ASP LYS LEU SEQRES 20 A 258 LYS ASN LYS TRP TRP TYR ASP LYS GLY GLU CYS HET GLU A 400 10 HET 4MP A 801 32 HET ZN A 1 1 HET ZN A 2 1 HETNAM GLU GLUTAMIC ACID HETNAM 4MP 1-(4-METHOXYBENZOYL)-2-PYRROLIDINONE HETNAM ZN ZINC ION HETSYN 4MP ANIRACETAM; 1-P-ANISOYL-2-PYRROLIDINONE FORMUL 2 GLU C5 H9 N O4 FORMUL 3 4MP C12 H13 N O3 FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *336(H2 O) HELIX 1 1 ASN A 22 LEU A 26 5 5 HELIX 2 2 GLU A 27 GLU A 30 5 4 HELIX 3 3 GLY A 34 ARG A 48 1 15 HELIX 4 4 ASN A 72 TYR A 80 1 9 HELIX 5 5 THR A 93 GLU A 98 1 6 HELIX 6 6 SER A 123 LYS A 129 1 7 HELIX 7 7 GLY A 141 SER A 150 1 10 HELIX 8 8 ILE A 152 ALA A 165 1 14 HELIX 9 9 THR A 173 SER A 184 1 12 HELIX 10 10 SER A 194 GLN A 202 1 9 HELIX 11 11 LEU A 230 GLN A 244 1 15 HELIX 12 12 GLY A 245 TYR A 256 1 12 SHEET 1 A 3 LYS A 50 ILE A 55 0 SHEET 2 A 3 THR A 5 THR A 10 1 N VAL A 8 O SER A 54 SHEET 3 A 3 ILE A 85 ALA A 86 1 O ILE A 85 N THR A 9 SHEET 1 B 2 MET A 18 TYR A 19 0 SHEET 2 B 2 TYR A 32 GLU A 33 -1 O GLU A 33 N MET A 18 SHEET 1 C 2 ILE A 100 PHE A 102 0 SHEET 2 C 2 ALA A 223 PRO A 225 -1 O THR A 224 N ASP A 101 SHEET 1 D 2 MET A 107 LEU A 109 0 SHEET 2 D 2 LYS A 218 TYR A 220 -1 O LYS A 218 N LEU A 109 SHEET 1 E 5 PHE A 170 THR A 171 0 SHEET 2 E 5 ALA A 134 LEU A 138 1 N THR A 137 O THR A 171 SHEET 3 E 5 PHE A 188 GLU A 193 1 O LEU A 191 N GLY A 136 SHEET 4 E 5 ILE A 111 LYS A 116 -1 N MET A 114 O PHE A 190 SHEET 5 E 5 THR A 208 VAL A 211 -1 O MET A 209 N ILE A 115 SSBOND 1 CYS A 206 CYS A 261 1555 1555 2.02 LINK ZN ZN A 1 NE2 HIS A 23 1555 1555 2.28 LINK ZN ZN A 2 OE1 GLU A 42 1555 1555 2.33 CISPEP 1 SER A 14 PRO A 15 0 -2.00 CISPEP 2 GLU A 166 PRO A 167 0 -7.39 CISPEP 3 LYS A 204 PRO A 205 0 6.61 SITE 1 AC1 13 TYR A 61 PRO A 89 LEU A 90 THR A 91 SITE 2 AC1 13 ARG A 96 LEU A 138 GLY A 141 SER A 142 SITE 3 AC1 13 THR A 143 GLU A 193 HOH A 352 HOH A 356 SITE 4 AC1 13 HOH A 365 SITE 1 AC2 8 PRO A 105 MET A 107 SER A 108 SER A 217 SITE 2 AC2 8 LYS A 218 GLY A 219 HOH A 290 HOH A 323 SITE 1 AC3 3 HIS A 23 GLU A 24 HOH A 291 SITE 1 AC4 2 GLU A 42 HIS A 46 CRYST1 47.060 47.364 137.409 90.00 90.00 90.00 P 2 2 21 4 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 0.021249 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007278 0.00000