HEADER MEMBRANE PROTEIN 02-MAR-11 3QXM TITLE CRYSTAL STRUCTURE OF HUMAN GLUK2 LIGAND-BINDING CORE IN COMPLEX WITH TITLE 2 NOVEL MARINE-DERIVED TOXINS, NEODYSIHERBAINE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 429-544,UNP RESIDUES 667-806; COMPND 5 SYNONYM: GLUK2,EXCITATORY AMINO ACID RECEPTOR 4,EAA4,GLUTAMATE COMPND 6 RECEPTOR 6,GLUR6; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: THE FUSION PROTEIN OF RESIDUES 429-544 OF GLUR-6, THE COMPND 9 LINKER GLY-THR AND 667-806 OF GLUR-6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GRIK2, GLUR6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TWO DOMAINS, LIGAND-BINDING, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.UNNO,M.SASAKI,M.IKEDA-SAITO REVDAT 3 01-NOV-23 3QXM 1 REMARK REVDAT 2 28-JUN-17 3QXM 1 SOURCE REVDAT 1 26-OCT-11 3QXM 0 JRNL AUTH M.UNNO,M.SHINOHARA,K.TAKAYAMA,H.TANAKA,K.TERUYA,K.DOH-URA, JRNL AUTH 2 R.SAKAI,M.SASAKI,M.IKEDA-SAITO JRNL TITL BINDING AND SELECTIVITY OF THE MARINE TOXIN NEODYSIHERBAINE JRNL TITL 2 A AND ITS SYNTHETIC ANALOGUES TO GLUK1 AND GLUK2 KAINATE JRNL TITL 3 RECEPTORS. JRNL REF J.MOL.BIOL. V. 413 667 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21893069 JRNL DOI 10.1016/J.JMB.2011.08.043 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 59382 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 + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3142 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3205 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 163 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4003 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 474 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.81000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : -1.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.619 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4216 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5720 ; 1.497 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 532 ; 5.586 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;34.125 ;24.208 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 777 ;13.177 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;15.281 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 646 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3117 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2555 ; 1.639 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4137 ; 2.633 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1661 ; 4.053 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1569 ; 6.343 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 401 A 513 REMARK 3 ORIGIN FOR THE GROUP (A): 0.0520 -18.7580 22.4150 REMARK 3 T TENSOR REMARK 3 T11: 0.0167 T22: 0.0280 REMARK 3 T33: 0.0366 T12: 0.0031 REMARK 3 T13: -0.0196 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.2178 L22: 0.9117 REMARK 3 L33: 1.1375 L12: -0.0028 REMARK 3 L13: -0.2081 L23: 0.1225 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: -0.0443 S13: -0.0648 REMARK 3 S21: -0.0522 S22: 0.0357 S23: 0.0143 REMARK 3 S31: 0.0534 S32: 0.0355 S33: -0.0542 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 600 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): -6.8090 13.9090 30.8590 REMARK 3 T TENSOR REMARK 3 T11: 0.4470 T22: 1.1436 REMARK 3 T33: 0.2018 T12: 0.1645 REMARK 3 T13: 0.1717 T23: 0.2874 REMARK 3 L TENSOR REMARK 3 L11: 147.7072 L22: 24.0832 REMARK 3 L33: 2.1450 L12: -1.1291 REMARK 3 L13: 17.4690 L23: 0.0389 REMARK 3 S TENSOR REMARK 3 S11: -2.6657 S12: -1.8783 S13: 1.8494 REMARK 3 S21: 0.8929 S22: 2.2280 S23: 0.4945 REMARK 3 S31: -0.1985 S32: -0.0064 S33: 0.4377 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 636 A 769 REMARK 3 ORIGIN FOR THE GROUP (A): 1.3390 -4.1900 25.1130 REMARK 3 T TENSOR REMARK 3 T11: 0.0429 T22: 0.0132 REMARK 3 T33: 0.0226 T12: -0.0016 REMARK 3 T13: 0.0114 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.0690 L22: 0.8608 REMARK 3 L33: 1.2131 L12: -0.0004 REMARK 3 L13: -0.1132 L23: 0.1087 REMARK 3 S TENSOR REMARK 3 S11: 0.0231 S12: -0.0060 S13: -0.0253 REMARK 3 S21: 0.0327 S22: 0.0393 S23: 0.0373 REMARK 3 S31: -0.1981 S32: 0.0686 S33: -0.0624 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 400 B 513 REMARK 3 ORIGIN FOR THE GROUP (A): 2.5390 23.6050 7.7790 REMARK 3 T TENSOR REMARK 3 T11: 0.0085 T22: 0.0226 REMARK 3 T33: 0.0303 T12: -0.0117 REMARK 3 T13: -0.0106 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.2752 L22: 0.8592 REMARK 3 L33: 1.1702 L12: -0.1159 REMARK 3 L13: -0.1984 L23: 0.0850 REMARK 3 S TENSOR REMARK 3 S11: -0.0227 S12: 0.0271 S13: 0.0674 REMARK 3 S21: -0.0130 S22: 0.0182 S23: 0.0236 REMARK 3 S31: -0.0461 S32: 0.0544 S33: 0.0046 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 600 B 601 REMARK 3 ORIGIN FOR THE GROUP (A): 1.0670 -9.1160 -2.8570 REMARK 3 T TENSOR REMARK 3 T11: 0.3516 T22: 0.0905 REMARK 3 T33: 0.0259 T12: -0.0659 REMARK 3 T13: -0.0176 T23: -0.0343 REMARK 3 L TENSOR REMARK 3 L11: 39.2664 L22: 68.4842 REMARK 3 L33: 8.8700 L12: 0.0000 REMARK 3 L13: -3.0635 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: -0.5644 S12: 1.4013 S13: -0.6081 REMARK 3 S21: -0.9421 S22: 0.3080 S23: -0.6628 REMARK 3 S31: 0.2100 S32: -0.6674 S33: 0.2563 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 636 B 774 REMARK 3 ORIGIN FOR THE GROUP (A): 5.6990 9.0230 5.8450 REMARK 3 T TENSOR REMARK 3 T11: 0.0603 T22: 0.0171 REMARK 3 T33: 0.0189 T12: 0.0082 REMARK 3 T13: -0.0028 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.1914 L22: 0.7763 REMARK 3 L33: 0.9601 L12: -0.1473 REMARK 3 L13: -0.3340 L23: 0.1962 REMARK 3 S TENSOR REMARK 3 S11: -0.0825 S12: -0.0222 S13: 0.0055 REMARK 3 S21: -0.0587 S22: 0.0151 S23: 0.0247 REMARK 3 S31: 0.1752 S32: 0.0729 S33: 0.0675 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3QXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 3G3F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-22% PEG4000, 2MM TRIS, 1MM EDTA, REMARK 280 10MM NACL, 10MM SODIUM L-ASCORBATE MONOHYDRATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 52.84200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 398 REMARK 465 ASN A 399 REMARK 465 GLY A 770 REMARK 465 ASN A 771 REMARK 465 GLY A 772 REMARK 465 CYS A 773 REMARK 465 PRO A 774 REMARK 465 GLU A 775 REMARK 465 SER B 398 REMARK 465 GLU B 775 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 ARG A 400 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 417 CG CD CE NZ REMARK 470 LYS A 420 CG CD CE NZ REMARK 470 LYS A 494 CG CD CE NZ REMARK 470 GLU A 691 CG CD OE1 OE2 REMARK 470 ASN B 399 CG OD1 ND2 REMARK 470 LYS B 420 CG CD CE NZ REMARK 470 ARG B 769 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 771 CG OD1 ND2 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 410 CD GLU A 410 OE2 0.085 REMARK 500 GLU B 410 CD GLU B 410 OE2 0.089 REMARK 500 GLU B 410 CD GLU B 410 OE2 0.072 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 409 112.69 -160.19 REMARK 500 GLU B 409 109.79 -160.78 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 781 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH B 782 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH B 791 DISTANCE = 7.03 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDZ A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDZ B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZNS RELATED DB: PDB REMARK 900 RELATED ID: 2ZNT RELATED DB: PDB REMARK 900 RELATED ID: 2ZNU RELATED DB: PDB REMARK 900 RELATED ID: 3FUZ RELATED DB: PDB REMARK 900 RELATED ID: 3FV1 RELATED DB: PDB REMARK 900 RELATED ID: 3FVG RELATED DB: PDB REMARK 900 RELATED ID: 3FVK RELATED DB: PDB REMARK 900 RELATED ID: 3FVN RELATED DB: PDB REMARK 900 RELATED ID: 3FVO RELATED DB: PDB DBREF 3QXM A 398 513 UNP Q13002 GRIK2_HUMAN 429 544 DBREF 3QXM A 636 775 UNP Q13002 GRIK2_HUMAN 667 806 DBREF 3QXM B 398 513 UNP Q13002 GRIK2_HUMAN 429 544 DBREF 3QXM B 636 775 UNP Q13002 GRIK2_HUMAN 667 806 SEQADV 3QXM GLY A 600 UNP Q13002 LINKER SEQADV 3QXM THR A 601 UNP Q13002 LINKER SEQADV 3QXM GLY B 600 UNP Q13002 LINKER SEQADV 3QXM THR B 601 UNP Q13002 LINKER SEQRES 1 A 258 SER ASN ARG SER LEU ILE VAL THR THR ILE LEU GLU GLU SEQRES 2 A 258 PRO TYR VAL LEU PHE LYS LYS SER ASP LYS PRO LEU TYR SEQRES 3 A 258 GLY ASN ASP ARG PHE GLU GLY TYR CYS ILE ASP LEU LEU SEQRES 4 A 258 ARG GLU LEU SER THR ILE LEU GLY PHE THR TYR GLU ILE SEQRES 5 A 258 ARG LEU VAL GLU ASP GLY LYS TYR GLY ALA GLN ASP ASP SEQRES 6 A 258 ALA ASN GLY GLN TRP ASN GLY MET VAL ARG GLU LEU ILE SEQRES 7 A 258 ASP HIS LYS ALA ASP LEU ALA VAL ALA PRO LEU ALA ILE SEQRES 8 A 258 THR TYR VAL ARG GLU LYS VAL ILE ASP PHE SER LYS PRO SEQRES 9 A 258 PHE MET THR LEU GLY ILE SER ILE LEU TYR ARG LYS GLY SEQRES 10 A 258 THR PRO ILE ASP SER ALA ASP ASP LEU ALA LYS GLN THR SEQRES 11 A 258 LYS ILE GLU TYR GLY ALA VAL GLU ASP GLY ALA THR MET SEQRES 12 A 258 THR PHE PHE LYS LYS SER LYS ILE SER THR TYR ASP LYS SEQRES 13 A 258 MET TRP ALA PHE MET SER SER ARG ARG GLN SER VAL LEU SEQRES 14 A 258 VAL LYS SER ASN GLU GLU GLY ILE GLN ARG VAL LEU THR SEQRES 15 A 258 SER ASP TYR ALA PHE LEU MET GLU SER THR THR ILE GLU SEQRES 16 A 258 PHE VAL THR GLN ARG ASN CYS ASN LEU THR GLN ILE GLY SEQRES 17 A 258 GLY LEU ILE ASP SER LYS GLY TYR GLY VAL GLY THR PRO SEQRES 18 A 258 MET GLY SER PRO TYR ARG ASP LYS ILE THR ILE ALA ILE SEQRES 19 A 258 LEU GLN LEU GLN GLU GLU GLY LYS LEU HIS MET MET LYS SEQRES 20 A 258 GLU LYS TRP TRP ARG GLY ASN GLY CYS PRO GLU SEQRES 1 B 258 SER ASN ARG SER LEU ILE VAL THR THR ILE LEU GLU GLU SEQRES 2 B 258 PRO TYR VAL LEU PHE LYS LYS SER ASP LYS PRO LEU TYR SEQRES 3 B 258 GLY ASN ASP ARG PHE GLU GLY TYR CYS ILE ASP LEU LEU SEQRES 4 B 258 ARG GLU LEU SER THR ILE LEU GLY PHE THR TYR GLU ILE SEQRES 5 B 258 ARG LEU VAL GLU ASP GLY LYS TYR GLY ALA GLN ASP ASP SEQRES 6 B 258 ALA ASN GLY GLN TRP ASN GLY MET VAL ARG GLU LEU ILE SEQRES 7 B 258 ASP HIS LYS ALA ASP LEU ALA VAL ALA PRO LEU ALA ILE SEQRES 8 B 258 THR TYR VAL ARG GLU LYS VAL ILE ASP PHE SER LYS PRO SEQRES 9 B 258 PHE MET THR LEU GLY ILE SER ILE LEU TYR ARG LYS GLY SEQRES 10 B 258 THR PRO ILE ASP SER ALA ASP ASP LEU ALA LYS GLN THR SEQRES 11 B 258 LYS ILE GLU TYR GLY ALA VAL GLU ASP GLY ALA THR MET SEQRES 12 B 258 THR PHE PHE LYS LYS SER LYS ILE SER THR TYR ASP LYS SEQRES 13 B 258 MET TRP ALA PHE MET SER SER ARG ARG GLN SER VAL LEU SEQRES 14 B 258 VAL LYS SER ASN GLU GLU GLY ILE GLN ARG VAL LEU THR SEQRES 15 B 258 SER ASP TYR ALA PHE LEU MET GLU SER THR THR ILE GLU SEQRES 16 B 258 PHE VAL THR GLN ARG ASN CYS ASN LEU THR GLN ILE GLY SEQRES 17 B 258 GLY LEU ILE ASP SER LYS GLY TYR GLY VAL GLY THR PRO SEQRES 18 B 258 MET GLY SER PRO TYR ARG ASP LYS ILE THR ILE ALA ILE SEQRES 19 B 258 LEU GLN LEU GLN GLU GLU GLY LYS LEU HIS MET MET LYS SEQRES 20 B 258 GLU LYS TRP TRP ARG GLY ASN GLY CYS PRO GLU HET NDZ A 301 20 HET NDZ B 302 20 HETNAM NDZ (2R,3AR,6R,7R,7AR)-2-[(2S)-2-AMINO-2-CARBOXYETHYL]-6,7- HETNAM 2 NDZ DIHYDROXYHEXAHYDRO-2H-FURO[3,2-B]PYRAN-2-CARBOXYLIC HETNAM 3 NDZ ACID FORMUL 3 NDZ 2(C11 H17 N O8) FORMUL 5 HOH *474(H2 O) HELIX 1 1 TYR A 423 ASP A 426 5 4 HELIX 2 2 GLY A 430 GLY A 444 1 15 HELIX 3 3 ASN A 468 ASP A 476 1 9 HELIX 4 4 THR A 489 LYS A 494 1 6 HELIX 5 5 SER A 639 LYS A 645 1 7 HELIX 6 6 GLY A 657 SER A 666 1 10 HELIX 7 7 ILE A 668 ARG A 681 1 14 HELIX 8 8 ARG A 681 LEU A 686 1 6 HELIX 9 9 SER A 689 SER A 700 1 12 HELIX 10 10 SER A 708 ASN A 718 1 11 HELIX 11 11 PRO A 742 GLU A 757 1 16 HELIX 12 12 GLY A 758 ARG A 769 1 12 HELIX 13 13 TYR B 423 ASP B 426 5 4 HELIX 14 14 GLY B 430 GLY B 444 1 15 HELIX 15 15 ASN B 468 ASP B 476 1 9 HELIX 16 16 THR B 489 LYS B 494 1 6 HELIX 17 17 SER B 639 LYS B 645 1 7 HELIX 18 18 GLY B 657 SER B 666 1 10 HELIX 19 19 ILE B 668 ARG B 681 1 14 HELIX 20 20 ARG B 681 LEU B 686 1 6 HELIX 21 21 SER B 689 SER B 700 1 12 HELIX 22 22 SER B 708 ASN B 718 1 11 HELIX 23 23 PRO B 742 GLU B 757 1 16 HELIX 24 24 GLY B 758 ARG B 769 1 12 SHEET 1 A 3 TYR A 447 LEU A 451 0 SHEET 2 A 3 LEU A 402 THR A 406 1 N VAL A 404 O GLU A 448 SHEET 3 A 3 LEU A 481 ALA A 482 1 O LEU A 481 N THR A 405 SHEET 1 B 2 LEU A 414 PHE A 415 0 SHEET 2 B 2 PHE A 428 GLU A 429 -1 O GLU A 429 N LEU A 414 SHEET 1 C 2 ILE A 496 PHE A 498 0 SHEET 2 C 2 GLY A 736 PRO A 738 -1 O THR A 737 N ASP A 497 SHEET 1 D 2 MET A 503 LEU A 505 0 SHEET 2 D 2 LYS A 731 TYR A 733 -1 O LYS A 731 N LEU A 505 SHEET 1 E 4 GLU A 650 GLY A 652 0 SHEET 2 E 4 TYR A 702 GLU A 707 1 O LEU A 705 N GLY A 652 SHEET 3 E 4 ILE A 507 ARG A 512 -1 N SER A 508 O MET A 706 SHEET 4 E 4 LEU A 721 ILE A 724 -1 O ILE A 724 N ILE A 509 SHEET 1 F 3 TYR B 447 LEU B 451 0 SHEET 2 F 3 LEU B 402 THR B 406 1 N VAL B 404 O GLU B 448 SHEET 3 F 3 LEU B 481 ALA B 482 1 O LEU B 481 N THR B 405 SHEET 1 G 2 LEU B 414 PHE B 415 0 SHEET 2 G 2 PHE B 428 GLU B 429 -1 O GLU B 429 N LEU B 414 SHEET 1 H 2 ILE B 496 PHE B 498 0 SHEET 2 H 2 GLY B 736 PRO B 738 -1 O THR B 737 N ASP B 497 SHEET 1 I 2 MET B 503 LEU B 505 0 SHEET 2 I 2 LYS B 731 TYR B 733 -1 O LYS B 731 N LEU B 505 SHEET 1 J 4 GLU B 650 GLY B 652 0 SHEET 2 J 4 TYR B 702 GLU B 707 1 O LEU B 705 N GLY B 652 SHEET 3 J 4 ILE B 507 ARG B 512 -1 N SER B 508 O MET B 706 SHEET 4 J 4 LEU B 721 ILE B 724 -1 O ILE B 724 N ILE B 509 SSBOND 1 CYS B 719 CYS B 773 1555 1555 2.05 CISPEP 1 GLU A 410 PRO A 411 0 0.35 CISPEP 2 GLU B 410 PRO B 411 0 1.89 CISPEP 3 GLU B 410 PRO B 411 0 0.53 SITE 1 AC1 15 HOH A 9 GLU A 409 TYR A 457 PRO A 485 SITE 2 AC1 15 LEU A 486 ALA A 487 ARG A 492 VAL A 654 SITE 3 AC1 15 GLY A 657 ALA A 658 THR A 659 ASN A 690 SITE 4 AC1 15 MET A 706 GLU A 707 THR A 710 SITE 1 AC2 15 HOH B 12 GLU B 409 TYR B 457 PRO B 485 SITE 2 AC2 15 LEU B 486 ALA B 487 ARG B 492 VAL B 654 SITE 3 AC2 15 GLY B 657 ALA B 658 THR B 659 ASN B 690 SITE 4 AC2 15 MET B 706 GLU B 707 THR B 710 CRYST1 46.353 105.684 57.999 90.00 102.27 90.00 P 1 21 1 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 0.021574 0.000000 0.004692 0.00000 SCALE2 0.000000 0.009462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017645 0.00000