HEADER RECEPTOR 22-JUN-07 2V3T TITLE STRUCTURE OF THE LIGAND-BINDING CORE OF THE IONOTROPIC GLUTAMATE TITLE 2 RECEPTOR-LIKE GLURDELTA2 IN THE APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RECEPTOR DELTA-2 SUBUNIT SYNONYM GLURDELTA2, GLUR COMPND 3 DELTA-2; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: LIGAND-BINDING CORE, RESIDUES 440-551 AND 664-813; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ORIGAMI 2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS MEMBRANE, RECEPTOR, TRANSPORT, GLYCOPROTEIN, POSTSYNAPTIC MEMBRANE, KEYWDS 2 IONOTROPIC GLUTAMATE RECEPTORS, MEMBRANE PROTEIN, LIGAND-BINDING KEYWDS 3 CORE, IONIC CHANNEL, ION TRANSPORT, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR P.NAUR,B.VESTERGAARD,M.GAJHEDE,J.S.KASTRUP REVDAT 7 23-OCT-24 2V3T 1 LINK REVDAT 6 24-JUL-19 2V3T 1 REMARK REVDAT 5 08-MAY-19 2V3T 1 REMARK LINK REVDAT 4 24-FEB-09 2V3T 1 VERSN REVDAT 3 11-SEP-07 2V3T 1 JRNL REVDAT 2 04-SEP-07 2V3T 1 JRNL REVDAT 1 07-AUG-07 2V3T 0 JRNL AUTH P.NAUR,K.B.HANSEN,A.S.KRISTENSEN,S.M.DRAVID,D.S.PICKERING, JRNL AUTH 2 L.OLSEN,B.VESTERGAARD,J.EGEBJERG,M.GAJHEDE,S.F.TRAYNELIS, JRNL AUTH 3 J.S.KASTRUP JRNL TITL IONOTROPIC GLUTAMATE-LIKE RECEPTOR {DELTA}2 BINDS D-SERINE JRNL TITL 2 AND GLYCINE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 14116 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17715062 JRNL DOI 10.1073/PNAS.0703718104 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 26508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1293 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 624 REMARK 3 BIN R VALUE (WORKING SET) : 0.4890 REMARK 3 BIN FREE R VALUE : 0.6256 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.143 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3990 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.05800 REMARK 3 B22 (A**2) : 2.18000 REMARK 3 B33 (A**2) : 5.87800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.55 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.53 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.65 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.437 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.560 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.950 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 37.51 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2V3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1290032784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27717 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 12.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11% PEG4000, 0.1 M TRIS-HCL PH 8.5, 50 REMARK 280 MM CACL2. HANGING DROP VAPOR DIFFUSION., VAPOR DIFFUSION, REMARK 280 HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 35.48550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.69650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.51550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.69650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.48550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.51550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.48550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.51550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 88.69650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.51550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.48550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 88.69650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.2 KCAL/MOL 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 400 REMARK 400 COMPOUND REMARK 400 RECEPTOR FOR GLUTAMATE. L-GLUTAMATE ACTS AS AN REMARK 400 EXCITATORY NEUROTRANSMITTER AT MANY SYNAPSES IN THE CENTRAL REMARK 400 NERVOUS SYSTEM. THE POSTSYNAPTIC ACTIONS OF GLU ARE MEDIATED REMARK 400 BY A VARIETY OF RECEPTORS THAT ARE NAMED ACCORDING TO REMARK 400 THEIR SELECTIVE AGONISTS. 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 1 REMARK 465 GLN A 62 REMARK 465 GLU A 63 REMARK 465 ASP A 64 REMARK 465 GLY A 65 REMARK 465 GLY A 114 REMARK 465 THR A 115 REMARK 465 PHE A 151 REMARK 465 GLU A 152 REMARK 465 ARG A 153 REMARK 465 ASP A 154 REMARK 465 ARG A 166 REMARK 465 SER A 167 REMARK 465 ASN A 168 REMARK 465 GLY A 169 REMARK 465 SER A 170 REMARK 465 GLU A 171 REMARK 465 GLY A 214 REMARK 465 ASN A 215 REMARK 465 LEU A 265 REMARK 465 GLY B 1 REMARK 465 GLY B 2 REMARK 465 GLY B 214 REMARK 465 ASN B 215 REMARK 465 ASN B 260 REMARK 465 GLY B 261 REMARK 465 GLN B 262 REMARK 465 CYS B 263 REMARK 465 ASP B 264 REMARK 465 LEU B 265 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 ASP A 264 CA C O CB CG OD1 OD2 REMARK 470 LYS B 259 CA C O CB CG CD CE REMARK 470 LYS B 259 NZ 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 PRO A 150 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 PRO A 150 C - N - CD ANGL. DEV. = -25.6 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 GLU A 12 113.49 -169.06 REMARK 500 ASN A 21 83.63 -163.77 REMARK 500 ALA A 85 35.23 -76.68 REMARK 500 THR A 99 -159.83 -90.42 REMARK 500 THR A 127 -15.59 -143.86 REMARK 500 THR A 133 -146.98 -128.01 REMARK 500 LEU A 148 50.62 -114.96 REMARK 500 ASN A 149 -85.34 -82.86 REMARK 500 LEU A 175 -163.17 178.76 REMARK 500 TYR A 189 135.62 -174.08 REMARK 500 TRP A 193 -171.36 -170.84 REMARK 500 ASN A 204 32.31 -93.70 REMARK 500 VAL A 217 158.00 65.47 REMARK 500 ARG A 220 -152.63 -168.61 REMARK 500 HIS A 228 112.91 -27.36 REMARK 500 LYS A 259 41.55 -90.37 REMARK 500 ASN A 260 51.55 -107.04 REMARK 500 GLN A 262 -78.09 -1.07 REMARK 500 CYS A 263 -144.11 -102.76 REMARK 500 LEU B 23 140.32 -24.67 REMARK 500 HIS B 56 19.14 52.65 REMARK 500 GLU B 63 6.32 -53.85 REMARK 500 ASN B 68 -164.77 -104.27 REMARK 500 SER B 84 -177.28 151.26 REMARK 500 ALA B 85 49.87 -73.17 REMARK 500 ARG B 113 140.73 -39.00 REMARK 500 SER B 116 44.79 -144.11 REMARK 500 THR B 133 -159.04 -137.16 REMARK 500 ASP B 136 18.75 56.85 REMARK 500 ARG B 166 -4.02 -47.81 REMARK 500 SER B 167 25.83 -168.33 REMARK 500 ASN B 168 26.63 80.30 REMARK 500 HIS B 228 117.96 -29.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1264 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 93 OE2 REMARK 620 2 GLU A 93 O 66.0 REMARK 620 3 VAL A 96 O 73.2 67.5 REMARK 620 4 ASP A 97 OD1 105.0 152.5 85.1 REMARK 620 5 ASP B 234 OD2 73.4 79.1 139.9 124.8 REMARK 620 6 ASP B 234 OD1 92.0 125.9 154.5 78.7 46.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1264 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 234 OD2 REMARK 620 2 ASP A 234 OD1 47.9 REMARK 620 3 GLU B 93 O 98.8 110.6 REMARK 620 4 GLU B 93 OE2 64.4 112.1 81.2 REMARK 620 5 VAL B 96 O 142.6 169.5 70.8 78.4 REMARK 620 6 ASP B 97 OD1 93.9 89.5 159.9 90.4 89.6 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B1264 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2V3U RELATED DB: PDB REMARK 900 STRUCTURE OF THE LIGAND-BINDING CORE OF THE IONOTROPIC GLUTAMATE REMARK 900 RECEPTOR-LIKE GLURDELTA2 IN COMPLEX WITH D-SERINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE NATIVE GLURDELTA2 IS A MEMBRANE PROTEIN. THE REMARK 999 CRYSTALLIZED PROTEIN IS A SE-MET DERIVATIVE OF THE REMARK 999 EXTRACELLULAR LIGAND-BINDING CORE OF GLURDELTA2. REMARK 999 TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REMARK 999 REPLACED WITH A GLY-THR LINKER. CONSEQUENTLY, THE PROTEIN REMARK 999 SEQUENCE MATCHES DISCONTINOUSLY WITH THE REFERENCE REMARK 999 DATABASE. THE FIRST GLYCINE IS A REMNANT OF A TRYPSIN REMARK 999 CLEAVAGE SITE. DBREF 2V3T A 1 1 PDB 2V3T 2V3T 1 1 DBREF 2V3T A 2 113 UNP Q63226 GRID2_RAT 440 551 DBREF 2V3T A 114 115 PDB 2V3T 2V3T 114 115 DBREF 2V3T A 116 265 UNP Q63226 GRID2_RAT 664 813 DBREF 2V3T B 1 1 PDB 2V3T 2V3T 1 1 DBREF 2V3T B 2 113 UNP Q63226 GRID2_RAT 440 551 DBREF 2V3T B 114 115 PDB 2V3T 2V3T 114 115 DBREF 2V3T B 116 265 UNP Q63226 GRID2_RAT 664 813 SEQRES 1 A 265 GLY GLY VAL VAL LEU ARG VAL VAL THR VAL LEU GLU GLU SEQRES 2 A 265 PRO PHE VAL MSE VAL SER GLU ASN VAL LEU GLY LYS PRO SEQRES 3 A 265 LYS LYS TYR GLN GLY PHE SER ILE ASP VAL LEU ASP ALA SEQRES 4 A 265 LEU SER ASN TYR LEU GLY PHE ASN TYR GLU ILE TYR VAL SEQRES 5 A 265 ALA PRO ASP HIS LYS TYR GLY SER PRO GLN GLU ASP GLY SEQRES 6 A 265 THR TRP ASN GLY LEU VAL GLY GLU LEU VAL PHE LYS ARG SEQRES 7 A 265 ALA ASP ILE GLY ILE SER ALA LEU THR ILE THR PRO ASP SEQRES 8 A 265 ARG GLU ASN VAL VAL ASP PHE THR THR ARG TYR MSE ASP SEQRES 9 A 265 TYR SER VAL GLY VAL LEU LEU ARG ARG GLY THR SER ILE SEQRES 10 A 265 GLN SER LEU GLN ASP LEU SER LYS GLN THR ASP ILE PRO SEQRES 11 A 265 TYR GLY THR VAL LEU ASP SER ALA VAL TYR GLN HIS VAL SEQRES 12 A 265 ARG MSE LYS GLY LEU ASN PRO PHE GLU ARG ASP SER MSE SEQRES 13 A 265 TYR SER GLN MSE TRP ARG MSE ILE ASN ARG SER ASN GLY SEQRES 14 A 265 SER GLU ASN ASN VAL LEU GLU SER GLN ALA GLY ILE GLN SEQRES 15 A 265 LYS VAL LYS TYR GLY ASN TYR ALA PHE VAL TRP ASP ALA SEQRES 16 A 265 ALA VAL LEU GLU TYR VAL ALA ILE ASN ASP PRO ASP CYS SEQRES 17 A 265 SER PHE TYR THR VAL GLY ASN THR VAL ALA ASP ARG GLY SEQRES 18 A 265 TYR GLY ILE ALA LEU GLN HIS GLY SER PRO TYR ARG ASP SEQRES 19 A 265 VAL PHE SER GLN ARG ILE LEU GLU LEU GLN GLN SER GLY SEQRES 20 A 265 ASP MSE ASP ILE LEU LYS HIS LYS TRP TRP PRO LYS ASN SEQRES 21 A 265 GLY GLN CYS ASP LEU SEQRES 1 B 265 GLY GLY VAL VAL LEU ARG VAL VAL THR VAL LEU GLU GLU SEQRES 2 B 265 PRO PHE VAL MSE VAL SER GLU ASN VAL LEU GLY LYS PRO SEQRES 3 B 265 LYS LYS TYR GLN GLY PHE SER ILE ASP VAL LEU ASP ALA SEQRES 4 B 265 LEU SER ASN TYR LEU GLY PHE ASN TYR GLU ILE TYR VAL SEQRES 5 B 265 ALA PRO ASP HIS LYS TYR GLY SER PRO GLN GLU ASP GLY SEQRES 6 B 265 THR TRP ASN GLY LEU VAL GLY GLU LEU VAL PHE LYS ARG SEQRES 7 B 265 ALA ASP ILE GLY ILE SER ALA LEU THR ILE THR PRO ASP SEQRES 8 B 265 ARG GLU ASN VAL VAL ASP PHE THR THR ARG TYR MSE ASP SEQRES 9 B 265 TYR SER VAL GLY VAL LEU LEU ARG ARG GLY THR SER ILE SEQRES 10 B 265 GLN SER LEU GLN ASP LEU SER LYS GLN THR ASP ILE PRO SEQRES 11 B 265 TYR GLY THR VAL LEU ASP SER ALA VAL TYR GLN HIS VAL SEQRES 12 B 265 ARG MSE LYS GLY LEU ASN PRO PHE GLU ARG ASP SER MSE SEQRES 13 B 265 TYR SER GLN MSE TRP ARG MSE ILE ASN ARG SER ASN GLY SEQRES 14 B 265 SER GLU ASN ASN VAL LEU GLU SER GLN ALA GLY ILE GLN SEQRES 15 B 265 LYS VAL LYS TYR GLY ASN TYR ALA PHE VAL TRP ASP ALA SEQRES 16 B 265 ALA VAL LEU GLU TYR VAL ALA ILE ASN ASP PRO ASP CYS SEQRES 17 B 265 SER PHE TYR THR VAL GLY ASN THR VAL ALA ASP ARG GLY SEQRES 18 B 265 TYR GLY ILE ALA LEU GLN HIS GLY SER PRO TYR ARG ASP SEQRES 19 B 265 VAL PHE SER GLN ARG ILE LEU GLU LEU GLN GLN SER GLY SEQRES 20 B 265 ASP MSE ASP ILE LEU LYS HIS LYS TRP TRP PRO LYS ASN SEQRES 21 B 265 GLY GLN CYS ASP LEU MODRES 2V3T MSE A 17 MET SELENOMETHIONINE MODRES 2V3T MSE A 103 MET SELENOMETHIONINE MODRES 2V3T MSE A 145 MET SELENOMETHIONINE MODRES 2V3T MSE A 156 MET SELENOMETHIONINE MODRES 2V3T MSE A 160 MET SELENOMETHIONINE MODRES 2V3T MSE A 163 MET SELENOMETHIONINE MODRES 2V3T MSE A 249 MET SELENOMETHIONINE MODRES 2V3T MSE B 17 MET SELENOMETHIONINE MODRES 2V3T MSE B 103 MET SELENOMETHIONINE MODRES 2V3T MSE B 145 MET SELENOMETHIONINE MODRES 2V3T MSE B 156 MET SELENOMETHIONINE MODRES 2V3T MSE B 160 MET SELENOMETHIONINE MODRES 2V3T MSE B 163 MET SELENOMETHIONINE MODRES 2V3T MSE B 249 MET SELENOMETHIONINE HET MSE A 17 8 HET MSE A 103 8 HET MSE A 145 8 HET MSE A 156 8 HET MSE A 160 8 HET MSE A 163 8 HET MSE A 249 8 HET MSE B 17 8 HET MSE B 103 8 HET MSE B 145 8 HET MSE B 156 8 HET MSE B 160 8 HET MSE B 163 8 HET MSE B 249 8 HET CA A1264 1 HET CA B1264 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 3 CA 2(CA 2+) FORMUL 5 HOH *30(H2 O) HELIX 1 1 GLY A 31 GLY A 45 1 15 HELIX 2 2 ASN A 68 PHE A 76 1 9 HELIX 3 3 THR A 89 VAL A 96 1 8 HELIX 4 4 SER A 119 SER A 124 1 6 HELIX 5 5 SER A 137 LEU A 148 1 12 HELIX 6 6 MSE A 156 ASN A 165 1 10 HELIX 7 7 SER A 177 GLY A 187 1 11 HELIX 8 8 ALA A 195 ASN A 204 1 10 HELIX 9 9 TYR A 232 GLY A 247 1 16 HELIX 10 10 GLY A 247 TRP A 257 1 11 HELIX 11 11 GLY B 31 GLY B 45 1 15 HELIX 12 12 ASN B 68 PHE B 76 1 9 HELIX 13 13 THR B 89 ASN B 94 1 6 HELIX 14 14 SER B 119 LYS B 125 1 7 HELIX 15 15 SER B 137 ASN B 149 1 13 HELIX 16 16 ASP B 154 ASN B 165 1 12 HELIX 17 17 GLU B 176 GLY B 187 1 12 HELIX 18 18 ALA B 195 ASN B 204 1 10 HELIX 19 19 TYR B 232 SER B 246 1 15 HELIX 20 20 GLY B 247 TRP B 257 1 11 SHEET 1 AA 5 ASN A 47 VAL A 52 0 SHEET 2 AA 5 VAL A 4 THR A 9 1 O LEU A 5 N GLU A 49 SHEET 3 AA 5 ILE A 81 THR A 87 1 O ILE A 81 N VAL A 8 SHEET 4 AA 5 ARG A 220 LEU A 226 -1 O GLY A 223 N SER A 84 SHEET 5 AA 5 ASP A 97 PHE A 98 -1 O ASP A 97 N LEU A 226 SHEET 1 AB 5 ASN A 47 VAL A 52 0 SHEET 2 AB 5 VAL A 4 THR A 9 1 O LEU A 5 N GLU A 49 SHEET 3 AB 5 ILE A 81 THR A 87 1 O ILE A 81 N VAL A 8 SHEET 4 AB 5 ARG A 220 LEU A 226 -1 O GLY A 223 N SER A 84 SHEET 5 AB 5 MSE A 103 TYR A 105 -1 O MSE A 103 N TYR A 222 SHEET 1 AC 2 MSE A 17 GLU A 20 0 SHEET 2 AC 2 LYS A 28 GLN A 30 -1 O LYS A 28 N SER A 19 SHEET 1 AD 4 TYR A 131 GLY A 132 0 SHEET 2 AD 4 ALA A 190 ASP A 194 1 O ALA A 190 N GLY A 132 SHEET 3 AD 4 VAL A 107 ARG A 112 -1 O GLY A 108 N TRP A 193 SHEET 4 AD 4 PHE A 210 VAL A 213 -1 O TYR A 211 N LEU A 111 SHEET 1 BA 5 ASN B 47 VAL B 52 0 SHEET 2 BA 5 VAL B 4 THR B 9 1 O LEU B 5 N GLU B 49 SHEET 3 BA 5 ILE B 81 ILE B 83 1 O ILE B 81 N VAL B 8 SHEET 4 BA 5 ALA B 225 GLN B 227 -1 O ALA B 225 N GLY B 82 SHEET 5 BA 5 VAL B 96 PHE B 98 -1 O ASP B 97 N LEU B 226 SHEET 1 BB 2 MSE B 17 GLU B 20 0 SHEET 2 BB 2 LYS B 28 GLN B 30 -1 O LYS B 28 N SER B 19 SHEET 1 BC 2 PRO B 61 GLN B 62 0 SHEET 2 BC 2 THR B 66 TRP B 67 -1 O THR B 66 N GLN B 62 SHEET 1 BD 4 TYR B 131 GLY B 132 0 SHEET 2 BD 4 ALA B 190 ASP B 194 1 O ALA B 190 N GLY B 132 SHEET 3 BD 4 MSE B 103 ARG B 112 -1 O GLY B 108 N TRP B 193 SHEET 4 BD 4 ALA B 218 TYR B 222 -1 N ASP B 219 O TYR B 105 SHEET 1 BE 4 TYR B 131 GLY B 132 0 SHEET 2 BE 4 ALA B 190 ASP B 194 1 O ALA B 190 N GLY B 132 SHEET 3 BE 4 MSE B 103 ARG B 112 -1 O GLY B 108 N TRP B 193 SHEET 4 BE 4 PHE B 210 VAL B 213 -1 O TYR B 211 N LEU B 111 SSBOND 1 CYS A 208 CYS A 263 1555 1555 2.04 LINK C VAL A 16 N MSE A 17 1555 1555 1.33 LINK C MSE A 17 N VAL A 18 1555 1555 1.32 LINK C TYR A 102 N MSE A 103 1555 1555 1.33 LINK C MSE A 103 N ASP A 104 1555 1555 1.33 LINK C ARG A 144 N MSE A 145 1555 1555 1.33 LINK C MSE A 145 N LYS A 146 1555 1555 1.33 LINK C SER A 155 N MSE A 156 1555 1555 1.33 LINK C MSE A 156 N TYR A 157 1555 1555 1.33 LINK C GLN A 159 N MSE A 160 1555 1555 1.33 LINK C MSE A 160 N TRP A 161 1555 1555 1.33 LINK C ARG A 162 N MSE A 163 1555 1555 1.33 LINK C MSE A 163 N ILE A 164 1555 1555 1.33 LINK C ASP A 248 N MSE A 249 1555 1555 1.33 LINK C MSE A 249 N ASP A 250 1555 1555 1.33 LINK C VAL B 16 N MSE B 17 1555 1555 1.33 LINK C MSE B 17 N VAL B 18 1555 1555 1.32 LINK C TYR B 102 N MSE B 103 1555 1555 1.33 LINK C MSE B 103 N ASP B 104 1555 1555 1.33 LINK C ARG B 144 N MSE B 145 1555 1555 1.33 LINK C MSE B 145 N LYS B 146 1555 1555 1.33 LINK C SER B 155 N MSE B 156 1555 1555 1.33 LINK C MSE B 156 N TYR B 157 1555 1555 1.33 LINK C GLN B 159 N MSE B 160 1555 1555 1.32 LINK C MSE B 160 N TRP B 161 1555 1555 1.32 LINK C ARG B 162 N MSE B 163 1555 1555 1.33 LINK C MSE B 163 N ILE B 164 1555 1555 1.33 LINK C ASP B 248 N MSE B 249 1555 1555 1.33 LINK C MSE B 249 N ASP B 250 1555 1555 1.33 LINK OE2 GLU A 93 CA CA A1264 1555 1555 2.42 LINK O GLU A 93 CA CA A1264 1555 1555 2.37 LINK O VAL A 96 CA CA A1264 1555 1555 2.41 LINK OD1 ASP A 97 CA CA A1264 1555 1555 2.29 LINK OD2 ASP A 234 CA CA B1264 1555 1555 2.49 LINK OD1 ASP A 234 CA CA B1264 1555 1555 2.86 LINK CA CA A1264 OD2 ASP B 234 1555 1555 3.01 LINK CA CA A1264 OD1 ASP B 234 1555 1555 2.14 LINK O GLU B 93 CA CA B1264 1555 1555 2.26 LINK OE2 GLU B 93 CA CA B1264 1555 1555 2.17 LINK O VAL B 96 CA CA B1264 1555 1555 2.55 LINK OD1 ASP B 97 CA CA B1264 1555 1555 2.40 CISPEP 1 GLU A 13 PRO A 14 0 -0.47 CISPEP 2 GLU B 13 PRO B 14 0 1.90 SITE 1 AC1 4 GLU A 93 VAL A 96 ASP A 97 ASP B 234 SITE 1 AC2 4 ASP A 234 GLU B 93 VAL B 96 ASP B 97 CRYST1 70.971 91.031 177.393 90.00 90.00 90.00 I 21 21 21 16 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 0.014090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005637 0.00000 MTRIX1 1 0.293800 -0.949600 0.109700 14.67000 1 MTRIX2 1 -0.944500 -0.306000 -0.119500 14.05000 1 MTRIX3 1 0.147100 -0.068470 -0.986800 -47.20000 1