HEADER MEMBRANE PROTEIN 01-JUN-11 3S9E TITLE CRYSTAL STRUCTURE OF THE KAINATE RECEPTOR GLUK3 LIGAND BINDING DOMAIN TITLE 2 IN COMPLEX WITH (S)-GLUTAMATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 3; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GRIK3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPINJ KEYWDS AGONIST, IONOTROPIC GLUTAMATE RECEPTOR, GLUTAMATE, MEMBRANE, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.VENSKUTONYTE,K.FRYDENVANG,M.GAJHEDE,J.S.KASTRUP REVDAT 6 13-SEP-23 3S9E 1 REMARK SEQADV LINK REVDAT 5 08-NOV-17 3S9E 1 REMARK REVDAT 4 09-AUG-17 3S9E 1 SOURCE REMARK REVDAT 3 02-OCT-13 3S9E 1 REMARK REVDAT 2 23-MAY-12 3S9E 1 REVDAT 1 28-SEP-11 3S9E 0 JRNL AUTH R.VENSKUTONYTE,K.FRYDENVANG,M.GAJHEDE,L.BUNCH,D.S.PICKERING, JRNL AUTH 2 J.S.KASTRUP JRNL TITL BINDING SITE AND INTERLOBE INTERACTIONS OF THE IONOTROPIC JRNL TITL 2 GLUTAMATE RECEPTOR GLUK3 LIGAND BINDING DOMAIN REVEALED BY JRNL TITL 3 HIGH RESOLUTION CRYSTAL STRUCTURE IN COMPLEX WITH JRNL TITL 4 (S)-GLUTAMATE. JRNL REF J.STRUCT.BIOL. V. 176 307 2011 JRNL REFN ISSN 1047-8477 JRNL PMID 21907808 JRNL DOI 10.1016/J.JSB.2011.08.014 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 72446 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3664 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 27.9008 - 4.7326 0.99 2700 136 0.1886 0.2032 REMARK 3 2 4.7326 - 3.7594 1.00 2656 150 0.1243 0.1687 REMARK 3 3 3.7594 - 3.2850 1.00 2669 155 0.1426 0.1615 REMARK 3 4 3.2850 - 2.9850 1.00 2649 135 0.1399 0.1722 REMARK 3 5 2.9850 - 2.7713 1.00 2659 141 0.1330 0.1715 REMARK 3 6 2.7713 - 2.6080 1.00 2623 157 0.1283 0.1806 REMARK 3 7 2.6080 - 2.4775 1.00 2692 132 0.1301 0.1959 REMARK 3 8 2.4775 - 2.3697 1.00 2639 133 0.1253 0.1683 REMARK 3 9 2.3697 - 2.2785 1.00 2660 141 0.1158 0.1607 REMARK 3 10 2.2785 - 2.1999 1.00 2638 147 0.1117 0.1671 REMARK 3 11 2.1999 - 2.1312 1.00 2667 136 0.1085 0.1857 REMARK 3 12 2.1312 - 2.0703 1.00 2615 151 0.1144 0.1699 REMARK 3 13 2.0703 - 2.0158 1.00 2662 155 0.1141 0.1695 REMARK 3 14 2.0158 - 1.9666 1.00 2623 140 0.1122 0.1686 REMARK 3 15 1.9666 - 1.9219 1.00 2665 145 0.1200 0.1980 REMARK 3 16 1.9219 - 1.8810 1.00 2598 146 0.1231 0.1832 REMARK 3 17 1.8810 - 1.8434 1.00 2723 117 0.1293 0.1795 REMARK 3 18 1.8434 - 1.8086 1.00 2617 148 0.1275 0.2006 REMARK 3 19 1.8086 - 1.7763 1.00 2620 145 0.1339 0.2156 REMARK 3 20 1.7763 - 1.7462 1.00 2652 134 0.1285 0.2071 REMARK 3 21 1.7462 - 1.7181 0.99 2672 145 0.1413 0.2442 REMARK 3 22 1.7181 - 1.6916 0.99 2579 136 0.1577 0.2629 REMARK 3 23 1.6916 - 1.6668 0.99 2631 140 0.1630 0.2343 REMARK 3 24 1.6668 - 1.6433 0.99 2655 139 0.1674 0.2562 REMARK 3 25 1.6433 - 1.6211 0.99 2615 128 0.1647 0.2336 REMARK 3 26 1.6211 - 1.6000 0.99 2603 132 0.1828 0.2713 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 1.01 REMARK 3 K_SOL : 0.46 REMARK 3 B_SOL : 38.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50330 REMARK 3 B22 (A**2) : 0.50330 REMARK 3 B33 (A**2) : -1.00660 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 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 : 0.013 4229 REMARK 3 ANGLE : 1.290 5705 REMARK 3 CHIRALITY : 0.079 631 REMARK 3 PLANARITY : 0.006 721 REMARK 3 DIHEDRAL : 13.848 1612 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: RESIDUES 1-2 (GP) AND RESIDUES 254-256 REMARK 3 (GSG) IN BOTH CHAINS WERE NOT LOCATED IN THE ELECTRON DENSITY REMARK 3 MAP. REMARK 4 REMARK 4 3S9E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000065926. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72508 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 27.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.42500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 1YCJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M SODIUM/POTASSIUM PHOSPHATE, PH REMARK 280 8.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 61.21500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.60750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.82250 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 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 PRO A 2 REMARK 465 GLY A 254 REMARK 465 SER A 255 REMARK 465 GLY A 256 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 GLY B 254 REMARK 465 SER B 255 REMARK 465 GLY B 256 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 O PRO A 258 O HOH A 804 2.08 REMARK 500 O SER B 225 O HOH B 725 2.12 REMARK 500 O PRO B 258 O HOH B 728 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 44 CD GLU A 44 OE1 -0.076 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 NA A 265 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 24 O REMARK 620 2 ARG A 26 O 83.0 REMARK 620 3 HOH A 348 O 88.1 118.1 REMARK 620 4 HOH A 362 O 150.8 83.0 76.2 REMARK 620 5 HOH A 369 O 111.3 158.1 80.0 90.3 REMARK 620 6 HOH A 522 O 55.0 124.6 96.9 150.1 59.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 264 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 5 O REMARK 620 2 SER B 52 OG 110.5 REMARK 620 3 HOH B 265 O 68.7 70.9 REMARK 620 4 HOH B 668 O 75.6 148.1 83.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 263 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 24 O REMARK 620 2 ARG B 26 O 83.6 REMARK 620 3 HOH B 304 O 59.9 128.2 REMARK 620 4 HOH B 359 O 152.6 83.4 144.1 REMARK 620 5 HOH B 405 O 89.4 118.7 97.8 76.1 REMARK 620 6 HOH B 480 O 114.9 155.5 58.8 85.4 79.2 REMARK 620 7 HOH B 484 O 108.7 80.0 79.0 92.5 156.0 78.9 REMARK 620 N 1 2 3 4 5 6 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 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLU B 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 264 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MH5 RELATED DB: PDB REMARK 900 SAME CRYSTAL STRUCTURE IN A DIFFERENT SPACE GROUP REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN REMARK 999 OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REMARK 999 REPLACED WITH A GLY-THR LINKER (RESIDUES 119 AND 120 OF THE REMARK 999 STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH REMARK 999 THE REFERENCE DATABASE (432-546, 669-806) DBREF 3S9E A 4 118 UNP P42264 GRIK3_RAT 432 546 DBREF 3S9E A 121 258 UNP P42264 GRIK3_RAT 669 806 DBREF 3S9E B 4 118 UNP P42264 GRIK3_RAT 432 546 DBREF 3S9E B 121 258 UNP P42264 GRIK3_RAT 669 806 SEQADV 3S9E GLY A 1 UNP P42264 EXPRESSION TAG SEQADV 3S9E PRO A 2 UNP P42264 EXPRESSION TAG SEQADV 3S9E GLY A 3 UNP P42264 EXPRESSION TAG SEQADV 3S9E GLY A 119 UNP P42264 LINKER SEQADV 3S9E THR A 120 UNP P42264 LINKER SEQADV 3S9E GLY B 1 UNP P42264 EXPRESSION TAG SEQADV 3S9E PRO B 2 UNP P42264 EXPRESSION TAG SEQADV 3S9E GLY B 3 UNP P42264 EXPRESSION TAG SEQADV 3S9E GLY B 119 UNP P42264 LINKER SEQADV 3S9E THR B 120 UNP P42264 LINKER SEQRES 1 A 258 GLY PRO GLY THR ASN ARG SER LEU ILE VAL THR THR LEU SEQRES 2 A 258 LEU GLU GLU PRO PHE VAL MET PHE ARG LYS SER ASP ARG SEQRES 3 A 258 THR LEU TYR GLY ASN ASP ARG PHE GLU GLY TYR CYS ILE SEQRES 4 A 258 ASP LEU LEU LYS GLU LEU ALA HIS ILE LEU GLY PHE SER SEQRES 5 A 258 TYR GLU ILE ARG LEU VAL GLU ASP GLY LYS TYR GLY ALA SEQRES 6 A 258 GLN ASP ASP LYS GLY GLN TRP ASN GLY MET VAL LYS GLU SEQRES 7 A 258 LEU ILE ASP HIS LYS ALA ASP LEU ALA VAL ALA PRO LEU SEQRES 8 A 258 THR ILE THR HIS VAL ARG GLU LYS ALA ILE ASP PHE SER SEQRES 9 A 258 LYS PRO PHE MET THR LEU GLY VAL SER ILE LEU TYR ARG SEQRES 10 A 258 LYS GLY THR PRO ILE ASP SER ALA ASP ASP LEU ALA LYS SEQRES 11 A 258 GLN THR LYS ILE GLU TYR GLY ALA VAL LYS ASP GLY ALA SEQRES 12 A 258 THR MET THR PHE PHE LYS LYS SER LYS ILE SER THR PHE SEQRES 13 A 258 GLU LYS MET TRP ALA PHE MET SER SER LYS PRO SER ALA SEQRES 14 A 258 LEU VAL LYS ASN ASN GLU GLU GLY ILE GLN ARG THR LEU SEQRES 15 A 258 THR ALA ASP TYR ALA LEU LEU MET GLU SER THR THR ILE SEQRES 16 A 258 GLU TYR ILE THR GLN ARG ASN CYS ASN LEU THR GLN ILE SEQRES 17 A 258 GLY GLY LEU ILE ASP SER LYS GLY TYR GLY ILE GLY THR SEQRES 18 A 258 PRO MET GLY SER PRO TYR ARG ASP LYS ILE THR ILE ALA SEQRES 19 A 258 ILE LEU GLN LEU GLN GLU GLU ASP LYS LEU HIS ILE MET SEQRES 20 A 258 LYS GLU LYS TRP TRP ARG GLY SER GLY CYS PRO SEQRES 1 B 258 GLY PRO GLY THR ASN ARG SER LEU ILE VAL THR THR LEU SEQRES 2 B 258 LEU GLU GLU PRO PHE VAL MET PHE ARG LYS SER ASP ARG SEQRES 3 B 258 THR LEU TYR GLY ASN ASP ARG PHE GLU GLY TYR CYS ILE SEQRES 4 B 258 ASP LEU LEU LYS GLU LEU ALA HIS ILE LEU GLY PHE SER SEQRES 5 B 258 TYR GLU ILE ARG LEU VAL GLU ASP GLY LYS TYR GLY ALA SEQRES 6 B 258 GLN ASP ASP LYS GLY GLN TRP ASN GLY MET VAL LYS GLU SEQRES 7 B 258 LEU ILE ASP HIS LYS ALA ASP LEU ALA VAL ALA PRO LEU SEQRES 8 B 258 THR ILE THR HIS VAL ARG GLU LYS ALA ILE ASP PHE SER SEQRES 9 B 258 LYS PRO PHE MET THR LEU GLY VAL SER ILE LEU TYR ARG SEQRES 10 B 258 LYS GLY THR PRO ILE ASP SER ALA ASP ASP LEU ALA LYS SEQRES 11 B 258 GLN THR LYS ILE GLU TYR GLY ALA VAL LYS ASP GLY ALA SEQRES 12 B 258 THR MET THR PHE PHE LYS LYS SER LYS ILE SER THR PHE SEQRES 13 B 258 GLU LYS MET TRP ALA PHE MET SER SER LYS PRO SER ALA SEQRES 14 B 258 LEU VAL LYS ASN ASN GLU GLU GLY ILE GLN ARG THR LEU SEQRES 15 B 258 THR ALA ASP TYR ALA LEU LEU MET GLU SER THR THR ILE SEQRES 16 B 258 GLU TYR ILE THR GLN ARG ASN CYS ASN LEU THR GLN ILE SEQRES 17 B 258 GLY GLY LEU ILE ASP SER LYS GLY TYR GLY ILE GLY THR SEQRES 18 B 258 PRO MET GLY SER PRO TYR ARG ASP LYS ILE THR ILE ALA SEQRES 19 B 258 ILE LEU GLN LEU GLN GLU GLU ASP LYS LEU HIS ILE MET SEQRES 20 B 258 LYS GLU LYS TRP TRP ARG GLY SER GLY CYS PRO HET GLU A 259 18 HET GOL A 260 6 HET CL A 261 1 HET CL A 262 1 HET PO4 A 263 5 HET PO4 A 264 5 HET NA A 265 1 HET GLU B 259 18 HET CL B 260 1 HET CL B 261 1 HET PO4 B 262 5 HET NA B 263 1 HET NA B 264 1 HETNAM GLU GLUTAMIC ACID HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GLU 2(C5 H9 N O4) FORMUL 4 GOL C3 H8 O3 FORMUL 5 CL 4(CL 1-) FORMUL 7 PO4 3(O4 P 3-) FORMUL 9 NA 3(NA 1+) FORMUL 16 HOH *581(H2 O) HELIX 1 1 TYR A 29 ASP A 32 5 4 HELIX 2 2 GLY A 36 GLY A 50 1 15 HELIX 3 3 ASN A 73 ASP A 81 1 9 HELIX 4 4 THR A 94 LYS A 99 1 6 HELIX 5 5 SER A 124 LYS A 130 1 7 HELIX 6 6 GLY A 142 SER A 151 1 10 HELIX 7 7 ILE A 153 SER A 164 1 12 HELIX 8 8 ASN A 173 ALA A 184 1 12 HELIX 9 9 SER A 192 ASN A 202 1 11 HELIX 10 10 TYR A 227 GLU A 241 1 15 HELIX 11 11 ASP A 242 ARG A 253 1 12 HELIX 12 12 TYR B 29 ASP B 32 5 4 HELIX 13 13 GLY B 36 GLY B 50 1 15 HELIX 14 14 ASN B 73 ASP B 81 1 9 HELIX 15 15 THR B 94 LYS B 99 1 6 HELIX 16 16 SER B 124 LYS B 130 1 7 HELIX 17 17 GLY B 142 SER B 151 1 10 HELIX 18 18 ILE B 153 SER B 164 1 12 HELIX 19 19 LYS B 166 LEU B 170 5 5 HELIX 20 20 ASN B 173 ALA B 184 1 12 HELIX 21 21 SER B 192 ASN B 202 1 11 HELIX 22 22 TYR B 227 GLU B 241 1 15 HELIX 23 23 ASP B 242 ARG B 253 1 12 SHEET 1 A 5 TYR A 53 LEU A 57 0 SHEET 2 A 5 LEU A 8 THR A 12 1 N VAL A 10 O ARG A 56 SHEET 3 A 5 LEU A 86 THR A 92 1 O LEU A 86 N THR A 11 SHEET 4 A 5 LYS A 215 PRO A 222 -1 O GLY A 220 N ALA A 87 SHEET 5 A 5 ILE A 101 PHE A 103 -1 N ASP A 102 O THR A 221 SHEET 1 B 5 TYR A 53 LEU A 57 0 SHEET 2 B 5 LEU A 8 THR A 12 1 N VAL A 10 O ARG A 56 SHEET 3 B 5 LEU A 86 THR A 92 1 O LEU A 86 N THR A 11 SHEET 4 B 5 LYS A 215 PRO A 222 -1 O GLY A 220 N ALA A 87 SHEET 5 B 5 MET A 108 LEU A 110 -1 N LEU A 110 O LYS A 215 SHEET 1 C 2 MET A 20 PHE A 21 0 SHEET 2 C 2 PHE A 34 GLU A 35 -1 O GLU A 35 N MET A 20 SHEET 1 D 4 GLU A 135 GLY A 137 0 SHEET 2 D 4 TYR A 186 GLU A 191 1 O LEU A 189 N GLY A 137 SHEET 3 D 4 VAL A 112 ARG A 117 -1 N LEU A 115 O LEU A 188 SHEET 4 D 4 LEU A 205 ILE A 208 -1 O THR A 206 N TYR A 116 SHEET 1 E 5 TYR B 53 LEU B 57 0 SHEET 2 E 5 LEU B 8 THR B 12 1 N VAL B 10 O ARG B 56 SHEET 3 E 5 LEU B 86 THR B 92 1 O LEU B 86 N THR B 11 SHEET 4 E 5 LYS B 215 PRO B 222 -1 O GLY B 220 N ALA B 87 SHEET 5 E 5 ILE B 101 PHE B 103 -1 N ASP B 102 O THR B 221 SHEET 1 F 5 TYR B 53 LEU B 57 0 SHEET 2 F 5 LEU B 8 THR B 12 1 N VAL B 10 O ARG B 56 SHEET 3 F 5 LEU B 86 THR B 92 1 O LEU B 86 N THR B 11 SHEET 4 F 5 LYS B 215 PRO B 222 -1 O GLY B 220 N ALA B 87 SHEET 5 F 5 MET B 108 LEU B 110 -1 N LEU B 110 O LYS B 215 SHEET 1 G 2 MET B 20 PHE B 21 0 SHEET 2 G 2 PHE B 34 GLU B 35 -1 O GLU B 35 N MET B 20 SHEET 1 H 4 GLU B 135 GLY B 137 0 SHEET 2 H 4 TYR B 186 GLU B 191 1 O LEU B 189 N GLY B 137 SHEET 3 H 4 VAL B 112 ARG B 117 -1 N LEU B 115 O LEU B 188 SHEET 4 H 4 LEU B 205 ILE B 208 -1 O THR B 206 N TYR B 116 SSBOND 1 CYS A 203 CYS A 257 1555 1555 2.05 SSBOND 2 CYS B 203 CYS B 257 1555 1555 2.04 LINK O SER A 24 NA NA A 265 1555 1555 2.86 LINK O ARG A 26 NA NA A 265 1555 1555 2.69 LINK NA NA A 265 O HOH A 348 1555 1555 2.85 LINK NA NA A 265 O HOH A 362 1555 1555 2.90 LINK NA NA A 265 O HOH A 369 1555 1555 2.64 LINK NA NA A 265 O HOH A 522 1555 1555 3.19 LINK O ASN B 5 NA NA B 264 1555 1555 2.70 LINK O SER B 24 NA NA B 263 1555 1555 2.93 LINK O ARG B 26 NA NA B 263 1555 1555 2.60 LINK OG SER B 52 NA NA B 264 1555 1555 2.83 LINK NA NA B 263 O HOH B 304 1555 1555 2.87 LINK NA NA B 263 O HOH B 359 1555 1555 2.85 LINK NA NA B 263 O HOH B 405 1555 1555 2.86 LINK NA NA B 263 O HOH B 480 1555 1555 2.80 LINK NA NA B 263 O HOH B 484 1555 1555 2.68 LINK NA NA B 264 O HOH B 265 1555 1555 3.02 LINK NA NA B 264 O HOH B 668 1555 1555 3.06 CISPEP 1 GLU A 16 PRO A 17 0 -3.67 CISPEP 2 GLU B 16 PRO B 17 0 -2.31 SITE 1 AC1 13 TYR A 63 PRO A 90 LEU A 91 THR A 92 SITE 2 AC1 13 ARG A 97 GLY A 142 ALA A 143 THR A 144 SITE 3 AC1 13 GLU A 191 HOH A 277 HOH A 296 HOH A 346 SITE 4 AC1 13 HOH A 384 SITE 1 AC2 7 LYS A 99 HOH A 355 HOH A 508 HOH A 759 SITE 2 AC2 7 THR B 109 HOH B 309 HOH B 558 SITE 1 AC3 4 GLN A 239 ASP A 242 LEU A 244 HIS A 245 SITE 1 AC4 2 ARG A 33 LEU A 57 SITE 1 AC5 4 LYS A 62 LYS A 140 HOH A 405 HOH A 751 SITE 1 AC6 2 LYS A 250 LYS B 250 SITE 1 AC7 6 SER A 24 ARG A 26 HOH A 348 HOH A 362 SITE 2 AC7 6 HOH A 369 HOH B 546 SITE 1 AC8 13 TYR B 63 PRO B 90 LEU B 91 THR B 92 SITE 2 AC8 13 ARG B 97 GLY B 142 ALA B 143 THR B 144 SITE 3 AC8 13 GLU B 191 HOH B 269 HOH B 276 HOH B 330 SITE 4 AC8 13 HOH B 371 SITE 1 AC9 4 GLN B 239 ASP B 242 LEU B 244 HIS B 245 SITE 1 BC1 3 ARG B 33 LEU B 57 HOH B 809 SITE 1 BC2 3 LYS B 62 LYS B 140 HOH B 754 SITE 1 BC3 7 SER B 24 ARG B 26 HOH B 304 HOH B 359 SITE 2 BC3 7 HOH B 405 HOH B 480 HOH B 484 SITE 1 BC4 8 ASN A 5 SER A 52 HOH A 266 HOH A 442 SITE 2 BC4 8 ASN B 5 SER B 52 HOH B 265 HOH B 668 CRYST1 67.800 67.800 122.430 90.00 90.00 90.00 P 41 8 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 0.014749 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014749 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008168 0.00000