HEADER TRANSPORT PROTEIN, RECEPTOR 30-OCT-13 4NF4 TITLE CRYSTAL STRUCTURE OF GLUN1/GLUN2A LIGAND-BINDING DOMAIN IN COMPLEX TITLE 2 WITH DCKA AND GLUTAMATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RECEPTOR IONOTROPIC, NMDA 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN, UNP RESIDUES 393-543; UNP RESIDUES COMPND 5 663-800; COMPND 6 SYNONYM: GLUN1, GLUTAMATE [NMDA] RECEPTOR SUBUNIT ZETA-1, N-METHYL-D- COMPND 7 ASPARTATE RECEPTOR SUBUNIT NR1, NMD-R1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: LIGAND-BINDING DOMAIN; UNP RESIDUES 402-539; UNP RESIDUES COMPND 13 661-802; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GRIN1, NMDAR1, RAT GLUN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMIB (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 13 ORGANISM_COMMON: RAT; SOURCE 14 ORGANISM_TAXID: 10116; SOURCE 15 GENE: GRIN2A; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RECEPTOR, DCKA AND GLUTAMATE, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ANNIE,N.TAJIMA,H.FURUKAWA REVDAT 2 09-AUG-17 4NF4 1 SOURCE REMARK REVDAT 1 12-MAR-14 4NF4 0 JRNL AUTH A.JESPERSEN,N.TAJIMA,G.FERNANDEZ-CUERVO,E.C.GARNIER-AMBLARD, JRNL AUTH 2 H.FURUKAWA JRNL TITL STRUCTURAL INSIGHTS INTO COMPETITIVE ANTAGONISM IN NMDA JRNL TITL 2 RECEPTORS. JRNL REF NEURON V. 81 366 2014 JRNL REFN ISSN 0896-6273 JRNL PMID 24462099 JRNL DOI 10.1016/J.NEURON.2013.11.033 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 44333 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2235 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 19.9042 - 5.0145 1.00 2805 162 0.1977 0.2053 REMARK 3 2 5.0145 - 3.9907 0.99 2701 129 0.1476 0.1738 REMARK 3 3 3.9907 - 3.4893 1.00 2663 150 0.1594 0.1888 REMARK 3 4 3.4893 - 3.1717 1.00 2683 124 0.1700 0.1640 REMARK 3 5 3.1717 - 2.9451 1.00 2644 136 0.1830 0.2309 REMARK 3 6 2.9451 - 2.7719 0.99 2601 152 0.1884 0.2350 REMARK 3 7 2.7719 - 2.6334 1.00 2616 150 0.1919 0.2671 REMARK 3 8 2.6334 - 2.5190 1.00 2629 136 0.1988 0.2200 REMARK 3 9 2.5190 - 2.4222 1.00 2616 142 0.2013 0.2569 REMARK 3 10 2.4222 - 2.3388 1.00 2590 145 0.1942 0.2414 REMARK 3 11 2.3388 - 2.2658 0.99 2591 153 0.1998 0.2338 REMARK 3 12 2.2658 - 2.2011 0.99 2582 136 0.2094 0.2818 REMARK 3 13 2.2011 - 2.1432 0.99 2597 122 0.2045 0.2440 REMARK 3 14 2.1432 - 2.0910 0.99 2584 135 0.2040 0.2712 REMARK 3 15 2.0910 - 2.0435 1.00 2624 131 0.2155 0.2633 REMARK 3 16 2.0435 - 2.0000 0.99 2572 132 0.2226 0.2606 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 4503 REMARK 3 ANGLE : 1.124 6089 REMARK 3 CHIRALITY : 0.081 678 REMARK 3 PLANARITY : 0.005 781 REMARK 3 DIHEDRAL : 15.727 1653 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 4NF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000083123. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44333 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.0 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG2000MME, HEPES, PH 7, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 27.12850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.07800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.74400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.07800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.12850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.74400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 MET A 2 REMARK 465 SER A 3 REMARK 465 THR A 50 REMARK 465 SER A 51 REMARK 465 PRO A 52 REMARK 465 ASN A 99 REMARK 465 ASN A 100 REMARK 465 SER A 101 REMARK 465 ASN A 102 REMARK 465 GLN A 288 REMARK 465 GLU A 289 REMARK 465 CYS A 290 REMARK 465 ASP A 291 REMARK 465 SER A 292 REMARK 465 SER B 4 REMARK 465 ASP B 5 REMARK 465 SER B 236 REMARK 465 GLY B 237 REMARK 465 HIS B 285 REMARK 465 ASN B 286 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 SER A 54 OG REMARK 470 HIS A 57 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 ARG A 155 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 169 CG OD1 OD2 REMARK 470 LYS A 200 CG CD CE NZ REMARK 470 ARG A 286 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 28 CG CD1 CD2 REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 SER B 150 OG REMARK 470 LYS B 152 CG CD CE NZ REMARK 470 SER B 161 OG REMARK 470 GLU B 274 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR A 4 CB CG2 REMARK 480 ARG A 5 CG CZ NH1 NH2 REMARK 480 LYS A 7 NZ REMARK 480 LYS A 29 CG CD CE NZ REMARK 480 GLU A 30 CG CD OE1 OE2 REMARK 480 VAL A 34 C O CB CG1 CG2 REMARK 480 ASN A 35 CG OD1 ND2 REMARK 480 ARG A 76 NE CZ NH1 NH2 REMARK 480 VAL A 98 CG1 CG2 REMARK 480 LYS A 103 N REMARK 480 LYS A 104 CD CE NZ REMARK 480 GLU A 105 CB CG CD OE1 OE2 REMARK 480 GLU A 130 CG CD OE1 OE2 REMARK 480 GLY A 153 C REMARK 480 LYS A 177 CD CE NZ REMARK 480 GLN A 178 CD OE1 NE2 REMARK 480 ARG A 196 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 204 CG CD OE1 OE2 REMARK 480 GLN A 211 CG NE2 REMARK 480 ARG A 214 CA REMARK 480 ASN A 216 CG OD1 ND2 REMARK 480 LYS A 217 CD CE NZ REMARK 480 GLN A 234 C O REMARK 480 LYS A 235 CD CE NZ REMARK 480 CYS A 236 N CB SG REMARK 480 ASP A 237 CG OD1 OD2 REMARK 480 VAL A 239 CG1 CG2 REMARK 480 GLU A 243 OE1 OE2 REMARK 480 ASP A 257 OD2 REMARK 480 GLN A 262 CD REMARK 480 ASP A 281 CG OD1 OD2 REMARK 480 LYS A 282 CE NZ REMARK 480 ASP B 6 CB CG OD1 OD2 REMARK 480 LEU B 28 CA CB REMARK 480 GLU B 30 CB CG CD OE1 OE2 REMARK 480 ARG B 34 NE CZ NH1 NH2 REMARK 480 LYS B 44 CD REMARK 480 LYS B 56 CD CE REMARK 480 ARG B 72 CD NE CZ NH1 NH2 REMARK 480 ARG B 195 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 208 CE NZ REMARK 480 GLU B 227 OE1 REMARK 480 LYS B 230 CG CD CE NZ REMARK 480 ILE B 234 CG1 CG2 CD1 REMARK 480 LYS B 251 CE REMARK 480 ARG B 257 CZ 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 OH TYR A 143 O THR B 243 1.85 REMARK 500 OG1 THR B 49 O HOH B 538 1.86 REMARK 500 O HOH B 699 O HOH B 714 1.89 REMARK 500 O HOH B 687 O HOH B 700 1.89 REMARK 500 O HOH B 630 O HOH B 679 1.91 REMARK 500 O HOH B 660 O HOH B 742 1.92 REMARK 500 O HOH A 625 O HOH A 626 1.93 REMARK 500 NZ LYS B 69 O HOH B 570 1.93 REMARK 500 O HOH A 535 O HOH A 559 1.93 REMARK 500 OH TYR B 105 O HOH B 750 1.96 REMARK 500 O HOH A 667 O HOH A 669 1.97 REMARK 500 O HOH B 680 O HOH B 706 1.99 REMARK 500 O HOH A 636 O HOH A 666 2.00 REMARK 500 O HOH B 697 O HOH B 702 2.04 REMARK 500 N TYR B 238 O HOH B 630 2.05 REMARK 500 O HOH B 726 O HOH B 761 2.07 REMARK 500 O ASN B 50 O HOH B 622 2.08 REMARK 500 O HOH B 654 O HOH B 673 2.08 REMARK 500 O HOH A 682 O HOH A 683 2.08 REMARK 500 NE2 GLN A 95 O HOH A 491 2.08 REMARK 500 O HOH A 657 O HOH B 711 2.08 REMARK 500 O HOH A 620 O HOH A 655 2.09 REMARK 500 O HOH A 605 O HOH A 675 2.11 REMARK 500 OE2 GLU B 276 O HOH B 482 2.12 REMARK 500 O HOH B 497 O HOH B 757 2.12 REMARK 500 NZ LYS B 251 O HOH B 662 2.13 REMARK 500 O HOH A 626 O HOH A 627 2.13 REMARK 500 O ASP A 49 O HOH A 665 2.15 REMARK 500 O HOH B 610 O HOH B 754 2.15 REMARK 500 O HOH B 677 O HOH B 746 2.16 REMARK 500 OE1 GLU B 271 O HOH B 570 2.16 REMARK 500 OE1 GLU B 23 O HOH B 579 2.16 REMARK 500 NZ LYS A 142 O HOH A 534 2.16 REMARK 500 O HOH B 681 O HOH B 708 2.17 REMARK 500 O HOH A 557 O HOH A 565 2.17 REMARK 500 O HOH A 638 O HOH A 651 2.17 REMARK 500 O HOH A 525 O HOH A 553 2.17 REMARK 500 OD1 ASN B 193 O HOH B 401 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 O HOH B 637 O HOH B 639 4455 2.10 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 ARG A 97 -163.03 -110.50 REMARK 500 ASN A 107 -169.02 -100.72 REMARK 500 LYS A 235 101.56 62.49 REMARK 500 CYS A 236 80.10 -171.25 REMARK 500 SER A 248 -135.00 -149.81 REMARK 500 GLU B 16 101.26 -167.41 REMARK 500 THR B 29 -37.39 161.44 REMARK 500 ARG B 34 -128.51 55.33 REMARK 500 LYS B 75 69.10 67.61 REMARK 500 LYS B 87 -111.67 -121.95 REMARK 500 TYR B 160 127.43 69.45 REMARK 500 ASN B 171 5.72 81.32 REMARK 500 THR B 243 -155.34 -145.24 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 2JK A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLU B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NF5 RELATED DB: PDB REMARK 900 RELATED ID: 4NF6 RELATED DB: PDB REMARK 900 RELATED ID: 4NF8 RELATED DB: PDB DBREF 4NF4 A 2 152 UNP P35439 NMDZ1_RAT 393 543 DBREF 4NF4 A 155 292 UNP P35439 NMDZ1_RAT 663 800 DBREF 4NF4 B 5 142 UNP Q00959 NMDE1_RAT 402 539 DBREF 4NF4 B 145 286 UNP Q00959 NMDE1_RAT 661 802 SEQADV 4NF4 GLY A 1 UNP P35439 EXPRESSION TAG SEQADV 4NF4 GLY A 153 UNP P35439 EXPRESSION TAG SEQADV 4NF4 THR A 154 UNP P35439 EXPRESSION TAG SEQADV 4NF4 SER B 4 UNP Q00959 EXPRESSION TAG SEQADV 4NF4 THR B 242 UNP Q00959 SER 758 ENGINEERED MUTATION SEQRES 1 A 292 GLY MET SER THR ARG LEU LYS ILE VAL THR ILE HIS GLN SEQRES 2 A 292 GLU PRO PHE VAL TYR VAL LYS PRO THR MET SER ASP GLY SEQRES 3 A 292 THR CYS LYS GLU GLU PHE THR VAL ASN GLY ASP PRO VAL SEQRES 4 A 292 LYS LYS VAL ILE CYS THR GLY PRO ASN ASP THR SER PRO SEQRES 5 A 292 GLY SER PRO ARG HIS THR VAL PRO GLN CYS CYS TYR GLY SEQRES 6 A 292 PHE CYS ILE ASP LEU LEU ILE LYS LEU ALA ARG THR MET SEQRES 7 A 292 ASN PHE THR TYR GLU VAL HIS LEU VAL ALA ASP GLY LYS SEQRES 8 A 292 PHE GLY THR GLN GLU ARG VAL ASN ASN SER ASN LYS LYS SEQRES 9 A 292 GLU TRP ASN GLY MET MET GLY GLU LEU LEU SER GLY GLN SEQRES 10 A 292 ALA ASP MET ILE VAL ALA PRO LEU THR ILE ASN ASN GLU SEQRES 11 A 292 ARG ALA GLN TYR ILE GLU PHE SER LYS PRO PHE LYS TYR SEQRES 12 A 292 GLN GLY LEU THR ILE LEU VAL LYS LYS GLY THR ARG ILE SEQRES 13 A 292 THR GLY ILE ASN ASP PRO ARG LEU ARG ASN PRO SER ASP SEQRES 14 A 292 LYS PHE ILE TYR ALA THR VAL LYS GLN SER SER VAL ASP SEQRES 15 A 292 ILE TYR PHE ARG ARG GLN VAL GLU LEU SER THR MET TYR SEQRES 16 A 292 ARG HIS MET GLU LYS HIS ASN TYR GLU SER ALA ALA GLU SEQRES 17 A 292 ALA ILE GLN ALA VAL ARG ASP ASN LYS LEU HIS ALA PHE SEQRES 18 A 292 ILE TRP ASP SER ALA VAL LEU GLU PHE GLU ALA SER GLN SEQRES 19 A 292 LYS CYS ASP LEU VAL THR THR GLY GLU LEU PHE PHE ARG SEQRES 20 A 292 SER GLY PHE GLY ILE GLY MET ARG LYS ASP SER PRO TRP SEQRES 21 A 292 LYS GLN ASN VAL SER LEU SER ILE LEU LYS SER HIS GLU SEQRES 22 A 292 ASN GLY PHE MET GLU ASP LEU ASP LYS THR TRP VAL ARG SEQRES 23 A 292 TYR GLN GLU CYS ASP SER SEQRES 1 B 283 SER ASP ASP ASN HIS LEU SER ILE VAL THR LEU GLU GLU SEQRES 2 B 283 ALA PRO PHE VAL ILE VAL GLU ASP ILE ASP PRO LEU THR SEQRES 3 B 283 GLU THR CYS VAL ARG ASN THR VAL PRO CYS ARG LYS PHE SEQRES 4 B 283 VAL LYS ILE ASN ASN SER THR ASN GLU GLY MET ASN VAL SEQRES 5 B 283 LYS LYS CYS CYS LYS GLY PHE CYS ILE ASP ILE LEU LYS SEQRES 6 B 283 LYS LEU SER ARG THR VAL LYS PHE THR TYR ASP LEU TYR SEQRES 7 B 283 LEU VAL THR ASN GLY LYS HIS GLY LYS LYS VAL ASN ASN SEQRES 8 B 283 VAL TRP ASN GLY MET ILE GLY GLU VAL VAL TYR GLN ARG SEQRES 9 B 283 ALA VAL MET ALA VAL GLY SER LEU THR ILE ASN GLU GLU SEQRES 10 B 283 ARG SER GLU VAL VAL ASP PHE SER VAL PRO PHE VAL GLU SEQRES 11 B 283 THR GLY ILE SER VAL MET VAL SER ARG GLY THR GLN VAL SEQRES 12 B 283 THR GLY LEU SER ASP LYS LYS PHE GLN ARG PRO HIS ASP SEQRES 13 B 283 TYR SER PRO PRO PHE ARG PHE GLY THR VAL PRO ASN GLY SEQRES 14 B 283 SER THR GLU ARG ASN ILE ARG ASN ASN TYR PRO TYR MET SEQRES 15 B 283 HIS GLN TYR MET THR ARG PHE ASN GLN ARG GLY VAL GLU SEQRES 16 B 283 ASP ALA LEU VAL SER LEU LYS THR GLY LYS LEU ASP ALA SEQRES 17 B 283 PHE ILE TYR ASP ALA ALA VAL LEU ASN TYR LYS ALA GLY SEQRES 18 B 283 ARG ASP GLU GLY CYS LYS LEU VAL THR ILE GLY SER GLY SEQRES 19 B 283 TYR ILE PHE ALA THR THR GLY TYR GLY ILE ALA LEU GLN SEQRES 20 B 283 LYS GLY SER PRO TRP LYS ARG GLN ILE ASP LEU ALA LEU SEQRES 21 B 283 LEU GLN PHE VAL GLY ASP GLY GLU MET GLU GLU LEU GLU SEQRES 22 B 283 THR LEU TRP LEU THR GLY ILE CYS HIS ASN HET 2JK A 301 16 HET GLU B 301 10 HETNAM 2JK 4-HYDROXY-5,7-DIMETHYLQUINOLINE-2-CARBOXYLIC ACID HETNAM GLU GLUTAMIC ACID FORMUL 3 2JK C12 H11 N O3 FORMUL 4 GLU C5 H9 N O4 FORMUL 5 HOH *657(H2 O) HELIX 1 1 GLY A 65 ASN A 79 1 15 HELIX 2 2 ASN A 107 SER A 115 1 9 HELIX 3 3 ASN A 128 GLN A 133 1 6 HELIX 4 4 ASP A 161 ASN A 166 1 6 HELIX 5 5 SER A 179 GLN A 188 1 10 HELIX 6 6 LEU A 191 LYS A 200 1 10 HELIX 7 7 SER A 205 ASP A 215 1 11 HELIX 8 8 SER A 225 SER A 233 1 9 HELIX 9 9 TRP A 260 ASN A 274 1 15 HELIX 10 10 GLY A 275 VAL A 285 1 11 HELIX 11 11 GLY B 61 LYS B 75 1 15 HELIX 12 12 ASN B 97 TYR B 105 1 9 HELIX 13 13 ASN B 118 GLU B 123 1 6 HELIX 14 14 ASP B 151 ARG B 156 1 6 HELIX 15 15 GLY B 172 TYR B 182 1 11 HELIX 16 16 TYR B 182 THR B 190 1 9 HELIX 17 17 ARG B 191 ASN B 193 5 3 HELIX 18 18 GLY B 196 THR B 206 1 11 HELIX 19 19 ALA B 216 GLY B 224 1 9 HELIX 20 20 TRP B 255 ASP B 269 1 15 HELIX 21 21 GLY B 270 THR B 281 1 12 SHEET 1 A 6 TYR A 18 PRO A 21 0 SHEET 2 A 6 THR A 58 TYR A 64 -1 O TYR A 64 N TYR A 18 SHEET 3 A 6 VAL A 42 PRO A 47 -1 N CYS A 44 O GLN A 61 SHEET 4 A 6 TYR A 82 LEU A 86 1 O LEU A 86 N THR A 45 SHEET 5 A 6 LEU A 6 THR A 10 1 N ILE A 8 O GLU A 83 SHEET 6 A 6 MET A 120 ILE A 121 1 O MET A 120 N VAL A 9 SHEET 1 B 2 GLN A 95 GLU A 96 0 SHEET 2 B 2 GLU A 105 TRP A 106 -1 O GLU A 105 N GLU A 96 SHEET 1 C 2 GLU A 136 PHE A 137 0 SHEET 2 C 2 GLY A 253 MET A 254 -1 O MET A 254 N GLU A 136 SHEET 1 D 4 TYR A 173 ALA A 174 0 SHEET 2 D 4 ALA A 220 ASP A 224 1 O ILE A 222 N ALA A 174 SHEET 3 D 4 LYS A 142 LYS A 151 -1 N LEU A 149 O PHE A 221 SHEET 4 D 4 LEU A 238 PHE A 250 -1 O VAL A 239 N VAL A 150 SHEET 1 E 8 ILE B 21 ASP B 24 0 SHEET 2 E 8 GLY B 52 LYS B 60 -1 O LYS B 60 N ILE B 21 SHEET 3 E 8 VAL B 37 LYS B 44 -1 N VAL B 37 O CYS B 59 SHEET 4 E 8 THR B 77 LEU B 82 1 O LEU B 82 N ARG B 40 SHEET 5 E 8 HIS B 8 THR B 13 1 N LEU B 9 O THR B 77 SHEET 6 E 8 MET B 110 ALA B 111 1 O MET B 110 N VAL B 12 SHEET 7 E 8 ALA B 248 LEU B 249 -1 O ALA B 248 N ALA B 111 SHEET 8 E 8 ASP B 126 PHE B 127 -1 N ASP B 126 O LEU B 249 SHEET 1 F 2 LYS B 91 VAL B 92 0 SHEET 2 F 2 VAL B 95 TRP B 96 -1 O VAL B 95 N VAL B 92 SHEET 1 G 4 PHE B 166 GLY B 167 0 SHEET 2 G 4 ALA B 211 ASP B 215 1 O ILE B 213 N GLY B 167 SHEET 3 G 4 VAL B 132 SER B 141 -1 N SER B 137 O TYR B 214 SHEET 4 G 4 LEU B 231 THR B 233 -1 O VAL B 232 N VAL B 140 SHEET 1 H 4 PHE B 166 GLY B 167 0 SHEET 2 H 4 ALA B 211 ASP B 215 1 O ILE B 213 N GLY B 167 SHEET 3 H 4 VAL B 132 SER B 141 -1 N SER B 137 O TYR B 214 SHEET 4 H 4 PHE B 240 TYR B 245 -1 O PHE B 240 N ILE B 136 SSBOND 1 CYS A 28 CYS A 62 1555 1555 2.06 SSBOND 2 CYS A 44 CYS A 63 1555 1555 2.04 SSBOND 3 CYS B 32 CYS B 58 1555 1555 2.05 SSBOND 4 CYS B 39 CYS B 59 1555 1555 2.05 SSBOND 5 CYS B 229 CYS B 284 1555 1555 2.05 CISPEP 1 GLU A 14 PRO A 15 0 3.58 CISPEP 2 LYS A 235 CYS A 236 0 -1.84 CISPEP 3 ALA B 17 PRO B 18 0 -0.19 CISPEP 4 SER B 161 PRO B 162 0 -2.82 SITE 1 AC1 16 GLN A 13 PHE A 16 PHE A 92 PRO A 124 SITE 2 AC1 16 LEU A 125 THR A 126 ARG A 131 TRP A 223 SITE 3 AC1 16 ASP A 224 VAL A 227 PHE A 250 HOH A 428 SITE 4 AC1 16 HOH A 445 HOH A 450 HOH A 503 HOH A 692 SITE 1 AC2 11 HIS B 88 SER B 114 THR B 116 ARG B 121 SITE 2 AC2 11 GLY B 172 SER B 173 THR B 174 TYR B 214 SITE 3 AC2 11 ASP B 215 HOH B 410 HOH B 429 CRYST1 54.257 87.488 136.156 90.00 90.00 90.00 P 21 21 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 0.018431 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007345 0.00000