HEADER TRANSFERASE 20-SEP-22 8B47 TITLE CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN TITLE 2 COMPLEX WITH A CYCLIC DI-ADENOSINE DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD KINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATP-DEPENDENT NAD KINASE; COMPND 5 EC: 2.7.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES EGD-E; SOURCE 3 ORGANISM_TAXID: 169963; SOURCE 4 GENE: NADK1, LMO0968; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TETRAMERIC NAD-KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GELIN,G.LABESSE REVDAT 2 31-JAN-24 8B47 1 REMARK REVDAT 1 11-JAN-23 8B47 0 JRNL AUTH D.A.CLEMENT,M.GELIN,C.LESEIGNEUR,V.HUTEAU,L.MONDANGE, JRNL AUTH 2 J.L.PONS,O.DUSSURGET,C.LIONNE,G.LABESSE,S.POCHET JRNL TITL SYNTHESIS AND STRUCTURE-ACTIVITY RELATIONSHIP STUDIES OF JRNL TITL 2 ORIGINAL CYCLIC DIADENOSINE DERIVATIVES AS NANOMOLAR JRNL TITL 3 INHIBITORS OF NAD KINASE FROM PATHOGENIC BACTERIA. JRNL REF EUR.J.MED.CHEM. V. 246 14941 2023 JRNL REFN ISSN 0223-5234 JRNL PMID 36455355 JRNL DOI 10.1016/J.EJMECH.2022.114941 REMARK 2 REMARK 2 RESOLUTION. 2.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 17478 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 3247 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 51.3900 - 7.1800 0.99 1289 143 0.2102 0.2207 REMARK 3 2 7.1700 - 5.7000 1.00 1284 138 0.2081 0.2861 REMARK 3 3 5.7000 - 4.9800 1.00 1304 139 0.1884 0.2992 REMARK 3 4 4.9800 - 4.5200 1.00 1287 142 0.1505 0.1724 REMARK 3 5 4.5200 - 4.2000 1.00 1267 138 0.1523 0.2101 REMARK 3 6 4.2000 - 3.9500 1.00 1321 147 0.1680 0.2098 REMARK 3 7 3.9500 - 3.7500 1.00 1311 143 0.1622 0.2716 REMARK 3 8 3.7500 - 3.5900 1.00 1283 148 0.1740 0.2149 REMARK 3 9 3.5900 - 3.4500 1.00 1278 140 0.1708 0.2422 REMARK 3 10 3.4500 - 3.3300 1.00 1290 144 0.2271 0.2872 REMARK 3 11 3.3300 - 3.2300 1.00 1281 146 0.2303 0.2601 REMARK 3 12 3.2300 - 3.1400 1.00 1305 148 0.2226 0.3012 REMARK 3 13 3.1400 - 3.0500 1.00 1272 141 0.2311 0.2790 REMARK 3 14 3.0500 - 2.9800 1.00 1319 148 0.2262 0.2928 REMARK 3 15 2.9800 - 2.9100 1.00 1295 143 0.2589 0.3043 REMARK 3 16 2.9100 - 2.8500 1.00 1282 146 0.2740 0.3279 REMARK 3 17 2.8500 - 2.7900 1.00 1280 142 0.2882 0.3568 REMARK 3 18 2.7900 - 2.7400 1.00 1299 144 0.3347 0.4539 REMARK 3 19 2.7400 - 2.6900 0.98 1279 144 0.3163 0.3644 REMARK 3 20 2.6900 - 2.6500 0.97 1206 135 0.2957 0.3686 REMARK 3 21 2.6500 - 2.6000 0.96 1256 143 0.3205 0.3878 REMARK 3 22 2.6000 - 2.5600 0.92 1185 137 0.3054 0.3087 REMARK 3 23 2.5600 - 2.5300 0.72 933 108 0.3061 0.3203 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 : 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.51 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0732 22.0401 -6.9716 REMARK 3 T TENSOR REMARK 3 T11: 0.3713 T22: 0.4287 REMARK 3 T33: 0.4285 T12: -0.0290 REMARK 3 T13: -0.0466 T23: 0.0250 REMARK 3 L TENSOR REMARK 3 L11: 4.0249 L22: 2.9001 REMARK 3 L33: 6.2279 L12: -0.9277 REMARK 3 L13: -1.1864 L23: -0.4168 REMARK 3 S TENSOR REMARK 3 S11: 0.1390 S12: 0.1753 S13: -0.0387 REMARK 3 S21: -0.1024 S22: -0.0628 S23: -0.2006 REMARK 3 S31: -0.0497 S32: 0.2182 S33: -0.0868 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 184 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9736 15.5140 11.8265 REMARK 3 T TENSOR REMARK 3 T11: 0.4433 T22: 0.3581 REMARK 3 T33: 0.5519 T12: -0.0093 REMARK 3 T13: 0.0272 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.1015 L22: 0.3008 REMARK 3 L33: 2.8686 L12: -0.1874 REMARK 3 L13: -0.1912 L23: -0.3148 REMARK 3 S TENSOR REMARK 3 S11: -0.0800 S12: -0.0647 S13: -0.0153 REMARK 3 S21: 0.0626 S22: 0.0452 S23: -0.0129 REMARK 3 S31: 0.1858 S32: 0.0374 S33: 0.0454 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 185 THROUGH 198 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7730 0.1918 27.3906 REMARK 3 T TENSOR REMARK 3 T11: 1.0878 T22: 0.4862 REMARK 3 T33: 0.7828 T12: -0.1998 REMARK 3 T13: 0.0585 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 6.7240 L22: 4.8513 REMARK 3 L33: 5.0997 L12: -4.3616 REMARK 3 L13: 2.0479 L23: -4.3334 REMARK 3 S TENSOR REMARK 3 S11: 0.4485 S12: -0.0542 S13: -1.1855 REMARK 3 S21: 2.7147 S22: -0.5143 S23: 0.7246 REMARK 3 S31: -1.0480 S32: 0.2628 S33: -0.0662 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 199 THROUGH 263 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7199 15.4964 12.1980 REMARK 3 T TENSOR REMARK 3 T11: 0.3682 T22: 0.3114 REMARK 3 T33: 0.4970 T12: 0.0203 REMARK 3 T13: 0.0218 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.9879 L22: 1.5282 REMARK 3 L33: 4.6042 L12: -0.0231 REMARK 3 L13: 0.4377 L23: -0.7036 REMARK 3 S TENSOR REMARK 3 S11: 0.1117 S12: 0.0835 S13: -0.0178 REMARK 3 S21: -0.0026 S22: -0.1158 S23: -0.2033 REMARK 3 S31: -0.1395 S32: 0.3435 S33: -0.0049 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0691 23.8979 28.6498 REMARK 3 T TENSOR REMARK 3 T11: 0.3807 T22: 0.4452 REMARK 3 T33: 0.4788 T12: 0.0465 REMARK 3 T13: 0.0350 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.5650 L22: 1.4705 REMARK 3 L33: 8.9265 L12: -0.0097 REMARK 3 L13: 0.7439 L23: 1.4506 REMARK 3 S TENSOR REMARK 3 S11: 0.0226 S12: -0.2141 S13: 0.1439 REMARK 3 S21: 0.1170 S22: -0.0761 S23: 0.0891 REMARK 3 S31: -0.6925 S32: -0.5305 S33: 0.0818 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 142 THROUGH 264 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3361 14.3977 13.7483 REMARK 3 T TENSOR REMARK 3 T11: 0.3455 T22: 0.3187 REMARK 3 T33: 0.4587 T12: 0.0550 REMARK 3 T13: 0.0291 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 2.8313 L22: 1.8827 REMARK 3 L33: 3.3718 L12: 0.0951 REMARK 3 L13: 0.7024 L23: -0.9205 REMARK 3 S TENSOR REMARK 3 S11: 0.1507 S12: 0.0279 S13: 0.0416 REMARK 3 S21: -0.0988 S22: -0.0710 S23: 0.0614 REMARK 3 S31: -0.0660 S32: -0.1046 S33: -0.0821 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 8B47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125650. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96770 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17576 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530 REMARK 200 RESOLUTION RANGE LOW (A) : 72.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.21800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 2.13400 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: 6RG9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 25 %(V/V) PEG 550 REMARK 280 MME, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 31.70300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.94250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.70300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.94250 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 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 70 REMARK 465 HIS A 71 REMARK 465 ILE A 111 REMARK 465 GLY A 112 REMARK 465 LYS A 113 REMARK 465 ASP A 264 REMARK 465 LEU A 265 REMARK 465 GLU A 266 REMARK 465 HIS A 267 REMARK 465 HIS A 268 REMARK 465 HIS A 269 REMARK 465 HIS A 270 REMARK 465 HIS A 271 REMARK 465 HIS A 272 REMARK 465 HIS B 71 REMARK 465 LEU B 72 REMARK 465 LEU B 265 REMARK 465 GLU B 266 REMARK 465 HIS B 267 REMARK 465 HIS B 268 REMARK 465 HIS B 269 REMARK 465 HIS B 270 REMARK 465 HIS B 271 REMARK 465 HIS B 272 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 LYS A 114 CG CD CE NZ REMARK 470 VAL A 191 CG1 CG2 REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 97 CG CD CE NZ REMARK 470 LYS B 113 CG CD CE NZ REMARK 470 ARG B 193 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 263 CG CD OE1 OE2 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 OE1 GLU A 123 O8 OWU A 301 2.16 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 58 38.39 -144.64 REMARK 500 TYR A 109 -148.58 -109.83 REMARK 500 ASN A 122 -72.01 -92.84 REMARK 500 ASN A 140 -113.16 54.88 REMARK 500 ALA A 162 -120.41 -94.46 REMARK 500 ALA A 185 68.81 39.85 REMARK 500 ASN A 189 -158.01 -120.47 REMARK 500 VAL A 191 -74.73 -102.57 REMARK 500 ASN A 213 -96.20 -124.74 REMARK 500 ASP A 222 -116.72 49.44 REMARK 500 GLU A 233 145.33 -171.92 REMARK 500 GLU A 237 149.33 -170.20 REMARK 500 ILE A 262 -69.13 -90.31 REMARK 500 ASN B 122 -70.38 -89.47 REMARK 500 ASN B 140 -106.44 57.99 REMARK 500 ALA B 162 -126.54 -108.52 REMARK 500 ALA B 185 65.28 37.18 REMARK 500 ASN B 189 -137.89 -141.54 REMARK 500 ASN B 213 -94.39 -125.34 REMARK 500 ASP B 222 -124.15 63.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ZZ7 RELATED DB: PDB DBREF 8B47 A 1 264 UNP Q8Y8D7 NADK1_LISMO 1 264 DBREF 8B47 B 1 264 UNP Q8Y8D7 NADK1_LISMO 1 264 SEQADV 8B47 LEU A 265 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 GLU A 266 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS A 272 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 LEU B 265 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 GLU B 266 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS B 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS B 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS B 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS B 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS B 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8B47 HIS B 272 UNP Q8Y8D7 EXPRESSION TAG SEQRES 1 A 272 MET LYS TYR MET ILE THR SER LYS GLY ASP GLU LYS SER SEQRES 2 A 272 ASP LEU LEU ARG LEU ASN MET ILE ALA GLY PHE GLY GLU SEQRES 3 A 272 TYR ASP MET GLU TYR ASP ASP VAL GLU PRO GLU ILE VAL SEQRES 4 A 272 ILE SER ILE GLY GLY ASP GLY THR PHE LEU SER ALA PHE SEQRES 5 A 272 HIS GLN TYR GLU GLU ARG LEU ASP GLU ILE ALA PHE ILE SEQRES 6 A 272 GLY ILE HIS THR GLY HIS LEU GLY PHE TYR ALA ASP TRP SEQRES 7 A 272 ARG PRO ALA GLU ALA ASP LYS LEU VAL LYS LEU LEU ALA SEQRES 8 A 272 LYS GLY GLU TYR GLN LYS VAL SER TYR PRO LEU LEU LYS SEQRES 9 A 272 THR THR VAL LYS TYR GLY ILE GLY LYS LYS GLU ALA THR SEQRES 10 A 272 TYR LEU ALA LEU ASN GLU SER THR VAL LYS SER SER GLY SEQRES 11 A 272 GLY PRO PHE VAL VAL ASP VAL VAL ILE ASN ASP ILE HIS SEQRES 12 A 272 PHE GLU ARG PHE ARG GLY ASP GLY LEU CYS MET SER THR SEQRES 13 A 272 PRO SER GLY THR THR ALA TYR ASN LYS SER LEU GLY GLY SEQRES 14 A 272 ALA LEU MET HIS PRO SER ILE GLU ALA MET GLN LEU THR SEQRES 15 A 272 GLU MET ALA SER ILE ASN ASN ARG VAL TYR ARG THR ILE SEQRES 16 A 272 GLY SER PRO LEU VAL PHE PRO LYS HIS HIS VAL VAL SER SEQRES 17 A 272 LEU GLN PRO VAL ASN ASP LYS ASP PHE GLN ILE SER VAL SEQRES 18 A 272 ASP HIS LEU SER ILE LEU HIS ARG ASP VAL GLN GLU ILE SEQRES 19 A 272 ARG TYR GLU VAL SER ALA LYS LYS ILE HIS PHE ALA ARG SEQRES 20 A 272 PHE ARG SER PHE PRO PHE TRP ARG ARG VAL HIS ASP SER SEQRES 21 A 272 PHE ILE GLU ASP LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 272 MET LYS TYR MET ILE THR SER LYS GLY ASP GLU LYS SER SEQRES 2 B 272 ASP LEU LEU ARG LEU ASN MET ILE ALA GLY PHE GLY GLU SEQRES 3 B 272 TYR ASP MET GLU TYR ASP ASP VAL GLU PRO GLU ILE VAL SEQRES 4 B 272 ILE SER ILE GLY GLY ASP GLY THR PHE LEU SER ALA PHE SEQRES 5 B 272 HIS GLN TYR GLU GLU ARG LEU ASP GLU ILE ALA PHE ILE SEQRES 6 B 272 GLY ILE HIS THR GLY HIS LEU GLY PHE TYR ALA ASP TRP SEQRES 7 B 272 ARG PRO ALA GLU ALA ASP LYS LEU VAL LYS LEU LEU ALA SEQRES 8 B 272 LYS GLY GLU TYR GLN LYS VAL SER TYR PRO LEU LEU LYS SEQRES 9 B 272 THR THR VAL LYS TYR GLY ILE GLY LYS LYS GLU ALA THR SEQRES 10 B 272 TYR LEU ALA LEU ASN GLU SER THR VAL LYS SER SER GLY SEQRES 11 B 272 GLY PRO PHE VAL VAL ASP VAL VAL ILE ASN ASP ILE HIS SEQRES 12 B 272 PHE GLU ARG PHE ARG GLY ASP GLY LEU CYS MET SER THR SEQRES 13 B 272 PRO SER GLY THR THR ALA TYR ASN LYS SER LEU GLY GLY SEQRES 14 B 272 ALA LEU MET HIS PRO SER ILE GLU ALA MET GLN LEU THR SEQRES 15 B 272 GLU MET ALA SER ILE ASN ASN ARG VAL TYR ARG THR ILE SEQRES 16 B 272 GLY SER PRO LEU VAL PHE PRO LYS HIS HIS VAL VAL SER SEQRES 17 B 272 LEU GLN PRO VAL ASN ASP LYS ASP PHE GLN ILE SER VAL SEQRES 18 B 272 ASP HIS LEU SER ILE LEU HIS ARG ASP VAL GLN GLU ILE SEQRES 19 B 272 ARG TYR GLU VAL SER ALA LYS LYS ILE HIS PHE ALA ARG SEQRES 20 B 272 PHE ARG SER PHE PRO PHE TRP ARG ARG VAL HIS ASP SER SEQRES 21 B 272 PHE ILE GLU ASP LEU GLU HIS HIS HIS HIS HIS HIS HET OWU A 301 50 HET 1PE A 302 38 HET PO4 A 303 5 HET OWU B 301 50 HET PO4 B 302 5 HETNAM OWU (1~{R},23~{R},24~{S},25~{R})-14-[[(2~{R},3~{S},4~{R}, HETNAM 2 OWU 5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN- HETNAM 3 OWU 2-YL]METHYL]-7-AZANYL-24,25-BIS(OXIDANYL)-20,20- HETNAM 4 OWU BIS(OXIDANYLIDENE)-26-OXA-20$L^{6}-THIA-2,4,6,9,14,17, HETNAM 5 OWU 21-HEPTAZATETRACYCLO[21.2.1.0^{2,10}.0^{3,8}]HEXACOSA- HETNAM 6 OWU 3,5,7,9-TETRAEN-11-YN-16-ONE HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM PO4 PHOSPHATE ION HETSYN 1PE PEG400 FORMUL 3 OWU 2(C27 H33 N13 O9 S) FORMUL 4 1PE C10 H22 O6 FORMUL 5 PO4 2(O4 P 3-) FORMUL 8 HOH *66(H2 O) HELIX 1 AA1 ASP A 10 GLY A 25 1 16 HELIX 2 AA2 GLY A 44 TYR A 55 1 12 HELIX 3 AA3 GLU A 56 ILE A 62 5 7 HELIX 4 AA4 ARG A 79 ALA A 81 5 3 HELIX 5 AA5 GLU A 82 LYS A 92 1 11 HELIX 6 AA6 PRO A 157 THR A 161 5 5 HELIX 7 AA7 ALA A 162 GLY A 168 1 7 HELIX 8 AA8 PRO A 252 ILE A 262 1 11 HELIX 9 AA9 ASP B 10 GLU B 26 1 17 HELIX 10 AB1 GLY B 44 TYR B 55 1 12 HELIX 11 AB2 ARG B 58 ILE B 62 5 5 HELIX 12 AB3 ARG B 79 ALA B 81 5 3 HELIX 13 AB4 GLU B 82 LYS B 92 1 11 HELIX 14 AB5 PRO B 157 THR B 161 5 5 HELIX 15 AB6 ALA B 162 LEU B 167 1 6 HELIX 16 AB7 PRO B 252 ILE B 262 1 11 SHEET 1 AA1 4 GLU A 30 TYR A 31 0 SHEET 2 AA1 4 LYS A 2 SER A 7 1 N TYR A 3 O GLU A 30 SHEET 3 AA1 4 ILE A 38 GLY A 43 1 O ILE A 40 N THR A 6 SHEET 4 AA1 4 ALA A 63 HIS A 68 1 O ILE A 67 N SER A 41 SHEET 1 AA2 6 GLU A 115 ALA A 120 0 SHEET 2 AA2 6 GLN A 96 LYS A 108 -1 N THR A 105 O TYR A 118 SHEET 3 AA2 6 GLU A 233 ARG A 247 -1 O ARG A 247 N GLN A 96 SHEET 4 AA2 6 VAL A 207 PRO A 211 -1 N LEU A 209 O ILE A 234 SHEET 5 AA2 6 PHE A 133 ILE A 139 -1 N VAL A 138 O SER A 208 SHEET 6 AA2 6 ILE A 142 GLY A 149 -1 O GLU A 145 N VAL A 137 SHEET 1 AA3 7 LEU A 224 HIS A 228 0 SHEET 2 AA3 7 PHE A 217 VAL A 221 -1 N VAL A 221 O LEU A 224 SHEET 3 AA3 7 GLU A 123 SER A 128 -1 N LYS A 127 O GLN A 218 SHEET 4 AA3 7 GLY A 151 SER A 155 -1 O MET A 154 N SER A 124 SHEET 5 AA3 7 ALA A 178 MET A 184 -1 O THR A 182 N CYS A 153 SHEET 6 AA3 7 LEU A 199 PRO A 202 -1 O PHE A 201 N MET A 179 SHEET 7 AA3 7 LEU B 171 MET B 172 1 O LEU B 171 N VAL A 200 SHEET 1 AA4 7 LEU A 171 MET A 172 0 SHEET 2 AA4 7 LEU B 199 PHE B 201 1 O VAL B 200 N LEU A 171 SHEET 3 AA4 7 MET B 179 MET B 184 -1 N LEU B 181 O LEU B 199 SHEET 4 AA4 7 GLY B 151 SER B 155 -1 N SER B 155 O GLN B 180 SHEET 5 AA4 7 GLU B 123 SER B 128 -1 N SER B 124 O MET B 154 SHEET 6 AA4 7 PHE B 217 VAL B 221 -1 O GLN B 218 N LYS B 127 SHEET 7 AA4 7 LEU B 224 HIS B 228 -1 O ILE B 226 N ILE B 219 SHEET 1 AA5 4 GLU B 30 TYR B 31 0 SHEET 2 AA5 4 LYS B 2 SER B 7 1 N TYR B 3 O GLU B 30 SHEET 3 AA5 4 ILE B 38 GLY B 43 1 O ILE B 40 N THR B 6 SHEET 4 AA5 4 ALA B 63 HIS B 68 1 O ILE B 67 N SER B 41 SHEET 1 AA6 2 GLN B 96 TYR B 100 0 SHEET 2 AA6 2 ILE B 243 ARG B 247 -1 O PHE B 245 N VAL B 98 SHEET 1 AA7 6 LYS B 114 ALA B 120 0 SHEET 2 AA7 6 LEU B 103 TYR B 109 -1 N THR B 105 O TYR B 118 SHEET 3 AA7 6 VAL B 231 VAL B 238 -1 O ARG B 235 N THR B 106 SHEET 4 AA7 6 VAL B 207 PRO B 211 -1 N VAL B 207 O TYR B 236 SHEET 5 AA7 6 PHE B 133 ILE B 139 -1 N VAL B 138 O SER B 208 SHEET 6 AA7 6 ILE B 142 GLY B 149 -1 O GLU B 145 N VAL B 137 CRYST1 63.406 145.885 54.904 90.00 90.00 90.00 P 21 21 2 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 0.015771 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006855 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018214 0.00000