HEADER TRANSFERASE 08-FEB-22 7R4M TITLE CRYSTAL STRUCTURE OF MITOCHONDRIAL NAD KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD KINASE 2, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MITOCHONDRIAL NAD KINASE,NAD KINASE DOMAIN-CONTAINING COMPND 5 PROTEIN 1,MITOCHONDRIAL; COMPND 6 EC: 2.7.1.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NADK2, C5ORF33, MNADK, NADKD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS NAD KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.LABESSE,C.MARY,M.GELIN,C.LIONNE REVDAT 4 01-MAY-24 7R4M 1 REMARK REVDAT 3 14-SEP-22 7R4M 1 JRNL REVDAT 2 03-AUG-22 7R4M 1 JRNL REVDAT 1 06-JUL-22 7R4M 0 JRNL AUTH C.MARY,M.H.SOFLAEE,R.KESAVAN,M.GELIN,H.BROWN,G.ZACHARIAS, JRNL AUTH 2 T.P.MATHEWS,A.LEMOFF,C.LIONNE,G.LABESSE,G.HOXHAJ JRNL TITL CRYSTAL STRUCTURE OF HUMAN NADK2 REVEALS A DIMERIC JRNL TITL 2 ORGANIZATION AND ACTIVE SITE OCCLUSION BY LYSINE JRNL TITL 3 ACETYLATION. JRNL REF MOL.CELL V. 82 3299 2022 JRNL REFN ISSN 1097-2765 JRNL PMID 35868311 JRNL DOI 10.1016/J.MOLCEL.2022.06.026 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 24666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 2047 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 40.5900 - 5.6500 0.97 1644 144 0.2221 0.2498 REMARK 3 2 5.6500 - 4.4900 0.99 1574 129 0.1541 0.1965 REMARK 3 3 4.4900 - 3.9200 1.00 1555 119 0.1482 0.1731 REMARK 3 4 3.9200 - 3.5600 0.99 1504 151 0.1700 0.2039 REMARK 3 5 3.5600 - 3.3100 1.00 1525 136 0.1846 0.2599 REMARK 3 6 3.3100 - 3.1100 1.00 1495 121 0.2029 0.2405 REMARK 3 7 3.1100 - 2.9600 1.00 1532 123 0.2264 0.2587 REMARK 3 8 2.9600 - 2.8300 1.00 1482 148 0.2488 0.2817 REMARK 3 9 2.8300 - 2.7200 1.00 1502 123 0.2319 0.2929 REMARK 3 10 2.7200 - 2.6200 1.00 1488 119 0.2487 0.3044 REMARK 3 11 2.6200 - 2.5400 0.99 1440 147 0.2403 0.2955 REMARK 3 12 2.5400 - 2.4700 1.00 1503 140 0.2714 0.2786 REMARK 3 13 2.4700 - 2.4100 1.00 1476 145 0.2869 0.3800 REMARK 3 14 2.4100 - 2.3500 1.00 1464 149 0.3105 0.3756 REMARK 3 15 2.3500 - 2.2900 0.99 1435 153 0.3204 0.3238 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.03 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 65 THROUGH 108 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0866 -6.3076 23.9807 REMARK 3 T TENSOR REMARK 3 T11: 0.3483 T22: 0.4928 REMARK 3 T33: 0.4546 T12: -0.0213 REMARK 3 T13: 0.1279 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 6.3516 L22: 7.4648 REMARK 3 L33: 1.9338 L12: -2.2385 REMARK 3 L13: 1.1762 L23: -1.8981 REMARK 3 S TENSOR REMARK 3 S11: -0.0983 S12: 0.4157 S13: 0.6840 REMARK 3 S21: -0.0459 S22: -0.5919 S23: -0.6856 REMARK 3 S31: -0.3039 S32: 0.9288 S33: 0.5242 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 109 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1105 -9.1496 30.8200 REMARK 3 T TENSOR REMARK 3 T11: 0.2895 T22: 0.4929 REMARK 3 T33: 0.3477 T12: -0.0686 REMARK 3 T13: 0.0353 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 6.2317 L22: 3.6015 REMARK 3 L33: 2.5004 L12: -1.4758 REMARK 3 L13: -0.3892 L23: 1.6462 REMARK 3 S TENSOR REMARK 3 S11: 0.1760 S12: -0.1534 S13: 0.5638 REMARK 3 S21: -0.2169 S22: -0.0368 S23: -0.4489 REMARK 3 S31: -0.3106 S32: 0.4422 S33: -0.0930 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 161 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.9202 -21.2832 30.2181 REMARK 3 T TENSOR REMARK 3 T11: 0.3511 T22: 0.5507 REMARK 3 T33: 0.4026 T12: -0.0204 REMARK 3 T13: 0.0006 T23: 0.0692 REMARK 3 L TENSOR REMARK 3 L11: 2.0900 L22: 2.5837 REMARK 3 L33: 3.1237 L12: -0.3119 REMARK 3 L13: -1.2237 L23: 0.8621 REMARK 3 S TENSOR REMARK 3 S11: -0.0070 S12: -0.1332 S13: -0.2300 REMARK 3 S21: 0.1250 S22: 0.0470 S23: 0.2257 REMARK 3 S31: 0.0966 S32: -0.0847 S33: -0.0476 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 222 THROUGH 377 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0094 -31.1970 6.7318 REMARK 3 T TENSOR REMARK 3 T11: 0.4205 T22: 0.4250 REMARK 3 T33: 0.4234 T12: -0.0525 REMARK 3 T13: -0.0512 T23: 0.0669 REMARK 3 L TENSOR REMARK 3 L11: 2.0981 L22: 2.2379 REMARK 3 L33: 3.8162 L12: 0.6922 REMARK 3 L13: 0.7704 L23: 0.0369 REMARK 3 S TENSOR REMARK 3 S11: 0.0736 S12: -0.0403 S13: -0.0844 REMARK 3 S21: -0.1056 S22: 0.1216 S23: 0.2930 REMARK 3 S31: 0.5083 S32: -0.4223 S33: -0.0946 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 378 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.2285 -35.7016 0.0391 REMARK 3 T TENSOR REMARK 3 T11: 0.6749 T22: 0.4803 REMARK 3 T33: 0.5499 T12: -0.0082 REMARK 3 T13: -0.0971 T23: -0.0743 REMARK 3 L TENSOR REMARK 3 L11: 4.3410 L22: 2.6587 REMARK 3 L33: 6.9351 L12: 0.0192 REMARK 3 L13: 1.7385 L23: -3.9009 REMARK 3 S TENSOR REMARK 3 S11: 0.2816 S12: 0.9753 S13: -0.9865 REMARK 3 S21: -0.7569 S22: 0.2782 S23: 0.4442 REMARK 3 S31: 1.3807 S32: -0.0508 S33: -0.5611 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 403 THROUGH 442 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.1717 -26.6835 14.0054 REMARK 3 T TENSOR REMARK 3 T11: 0.3657 T22: 0.3981 REMARK 3 T33: 0.4152 T12: 0.0191 REMARK 3 T13: -0.0227 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 2.2460 L22: 1.9231 REMARK 3 L33: 3.7092 L12: 0.8749 REMARK 3 L13: -0.6140 L23: -0.9135 REMARK 3 S TENSOR REMARK 3 S11: -0.0014 S12: 0.1195 S13: -0.0914 REMARK 3 S21: -0.0338 S22: -0.0201 S23: -0.0600 REMARK 3 S31: -0.0948 S32: 0.1088 S33: 0.0764 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 7R4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120878. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24750 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 50.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 1.21900 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: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400 28% V/V, CACL2 150 MM, 0.1 M REMARK 280 SODIUM HEPES, 2% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 111.71000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.23500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.23500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 167.56500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.23500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.23500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.85500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.23500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.23500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 167.56500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.23500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.23500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.85500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 111.71000 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: 7230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 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 MET A 52 REMARK 465 GLY A 53 REMARK 465 HIS A 54 REMARK 465 HIS A 55 REMARK 465 HIS A 56 REMARK 465 HIS A 57 REMARK 465 HIS A 58 REMARK 465 HIS A 59 REMARK 465 GLY A 60 REMARK 465 ARG A 61 REMARK 465 ALA A 62 REMARK 465 ASP A 63 REMARK 465 GLY A 64 REMARK 465 ARG A 86 REMARK 465 TYR A 87 REMARK 465 ARG A 88 REMARK 465 TYR A 89 REMARK 465 ALA A 90 REMARK 465 GLU A 91 REMARK 465 LEU A 92 REMARK 465 SER A 93 REMARK 465 GLU A 94 REMARK 465 GLU A 95 REMARK 465 ASP A 96 REMARK 465 LEU A 97 REMARK 465 LYS A 98 REMARK 465 GLN A 99 REMARK 465 LEU A 100 REMARK 465 LEU A 101 REMARK 465 ALA A 102 REMARK 465 GLN A 241 REMARK 465 GLN A 242 REMARK 465 LEU A 243 REMARK 465 SER A 244 REMARK 465 LEU A 245 REMARK 465 ASN A 246 REMARK 465 GLN A 247 REMARK 465 HIS A 248 REMARK 465 ASN A 249 REMARK 465 ARG A 250 REMARK 465 ALA A 251 REMARK 465 LEU A 252 REMARK 465 ASN A 253 REMARK 465 ILE A 254 REMARK 465 GLU A 255 REMARK 465 ARG A 256 REMARK 465 ALA A 257 REMARK 465 HIS A 258 REMARK 465 ASP A 259 REMARK 465 GLU A 260 REMARK 465 ARG A 261 REMARK 465 SER A 262 REMARK 465 GLU A 263 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 GLN A 85 CG CD OE1 NE2 REMARK 470 TYR A 108 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 109 OG REMARK 470 ARG A 340 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 343 CG OD1 ND2 REMARK 470 LEU A 344 CG CD1 CD2 REMARK 470 LEU A 346 CG CD1 CD2 REMARK 470 LEU A 348 CG CD1 CD2 REMARK 470 GLU A 351 CG CD OE1 OE2 REMARK 470 ARG A 384 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 386 CG CD1 CD2 CE1 CE2 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 O GLN A 442 O HOH A 601 1.57 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 A 601 O HOH A 718 6445 2.13 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 LYS A 104 -96.18 -101.60 REMARK 500 SER A 107 -161.83 -164.44 REMARK 500 TYR A 108 -79.28 57.65 REMARK 500 ASN A 276 -66.86 -96.71 REMARK 500 SER A 306 31.97 -92.92 REMARK 500 ALA A 318 -133.37 -90.04 REMARK 500 GLN A 341 49.62 -95.68 REMARK 500 LEU A 344 37.50 -72.20 REMARK 500 SER A 345 -151.42 48.79 REMARK 500 LEU A 346 156.73 66.17 REMARK 500 ALA A 382 -89.03 -94.98 REMARK 500 ASN A 383 -160.42 40.20 REMARK 500 SER A 389 -115.40 -105.81 REMARK 500 ASP A 406 69.41 -153.96 REMARK 500 PHE A 419 73.85 -152.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAP A 501 O1A REMARK 620 2 NAP A 501 O1N 77.8 REMARK 620 3 NAP A 501 O3X 97.6 85.6 REMARK 620 4 HOH A 721 O 176.3 99.2 84.4 REMARK 620 5 HOH A 726 O 93.7 96.5 168.7 84.3 REMARK 620 6 HOH A 728 O 97.5 175.3 94.3 85.5 84.6 REMARK 620 N 1 2 3 4 5 DBREF 7R4M A 61 442 UNP Q4G0N4 NAKD2_HUMAN 61 442 SEQADV 7R4M MET A 52 UNP Q4G0N4 INITIATING METHIONINE SEQADV 7R4M GLY A 53 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4M HIS A 54 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4M HIS A 55 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4M HIS A 56 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4M HIS A 57 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4M HIS A 58 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4M HIS A 59 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4M GLY A 60 UNP Q4G0N4 EXPRESSION TAG SEQRES 1 A 391 MET GLY HIS HIS HIS HIS HIS HIS GLY ARG ALA ASP GLY SEQRES 2 A 391 GLY PHE ARG PRO SER ARG VAL VAL VAL VAL ALA LYS THR SEQRES 3 A 391 THR ARG TYR GLU PHE GLU GLN GLN ARG TYR ARG TYR ALA SEQRES 4 A 391 GLU LEU SER GLU GLU ASP LEU LYS GLN LEU LEU ALA LEU SEQRES 5 A 391 LYS GLY SER SER TYR SER GLY LEU LEU GLU ARG HIS HIS SEQRES 6 A 391 ILE HIS THR LYS ASN VAL GLU HIS ILE ILE ASP SER LEU SEQRES 7 A 391 ARG ASN GLU GLY ILE GLU VAL ARG LEU VAL LYS ARG ARG SEQRES 8 A 391 GLU TYR ASP GLU GLU THR VAL ARG TRP ALA ASP ALA VAL SEQRES 9 A 391 ILE ALA ALA GLY GLY ASP GLY THR MET LEU LEU ALA ALA SEQRES 10 A 391 SER LYS VAL LEU ASP ARG LEU LYS PRO VAL ILE GLY VAL SEQRES 11 A 391 ASN THR ASP PRO GLU ARG SER GLU GLY HIS LEU CYS LEU SEQRES 12 A 391 PRO VAL ARG TYR THR HIS SER PHE PRO GLU ALA LEU GLN SEQRES 13 A 391 LYS PHE TYR ARG GLY GLU PHE ARG TRP LEU TRP ARG GLN SEQRES 14 A 391 ARG ILE ARG LEU TYR LEU GLU GLY THR GLY ILE ASN PRO SEQRES 15 A 391 VAL PRO VAL ASP LEU HIS GLU GLN GLN LEU SER LEU ASN SEQRES 16 A 391 GLN HIS ASN ARG ALA LEU ASN ILE GLU ARG ALA HIS ASP SEQRES 17 A 391 GLU ARG SER GLU ALA SER GLY PRO GLN LEU LEU PRO VAL SEQRES 18 A 391 ARG ALA LEU ASN GLU VAL PHE ILE GLY GLU SER LEU SER SEQRES 19 A 391 SER ARG ALA SER TYR TYR GLU ILE SER VAL ASP ASP GLY SEQRES 20 A 391 PRO TRP GLU LYS GLN LYS SER SER GLY LEU ASN LEU CYS SEQRES 21 A 391 THR GLY THR GLY SER LYS ALA TRP SER PHE ASN ILE ASN SEQRES 22 A 391 ARG VAL ALA THR GLN ALA VAL GLU ASP VAL LEU ASN ILE SEQRES 23 A 391 ALA LYS ARG GLN GLY ASN LEU SER LEU PRO LEU ASN ARG SEQRES 24 A 391 GLU LEU VAL GLU LYS VAL THR ASN GLU TYR ASN GLU SER SEQRES 25 A 391 LEU LEU TYR SER PRO GLU GLU PRO LYS ILE LEU PHE SER SEQRES 26 A 391 ILE ARG GLU PRO ILE ALA ASN ARG VAL PHE SER SER SER SEQRES 27 A 391 ARG GLN ARG CYS PHE SER SER LYS VAL CYS VAL ARG SER SEQRES 28 A 391 ARG CYS TRP ASP ALA CYS MET VAL VAL ASP GLY GLY THR SEQRES 29 A 391 SER PHE GLU PHE ASN ASP GLY ALA ILE ALA SER MET MET SEQRES 30 A 391 ILE ASN LYS GLU ASP GLU LEU ARG THR VAL LEU LEU GLU SEQRES 31 A 391 GLN HET NAP A 501 48 HET CA A 502 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM CA CALCIUM ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 CA CA 2+ FORMUL 4 HOH *152(H2 O) HELIX 1 AA1 THR A 78 GLN A 85 1 8 HELIX 2 AA2 TYR A 108 GLU A 132 1 25 HELIX 3 AA3 ARG A 142 TYR A 144 5 3 HELIX 4 AA4 ASP A 145 ALA A 152 1 8 HELIX 5 AA5 GLY A 160 LYS A 170 1 11 HELIX 6 AA6 PRO A 195 HIS A 200 5 6 HELIX 7 AA7 SER A 201 ARG A 211 1 11 HELIX 8 AA8 GLY A 313 LYS A 317 5 5 HELIX 9 AA9 ALA A 318 ARG A 325 1 8 HELIX 10 AB1 ALA A 327 GLN A 341 1 15 HELIX 11 AB2 ASN A 349 SER A 363 1 15 HELIX 12 AB3 LYS A 431 GLU A 434 5 4 SHEET 1 AA1 4 GLU A 135 LYS A 140 0 SHEET 2 AA1 4 ARG A 70 ALA A 75 1 N VAL A 73 O VAL A 139 SHEET 3 AA1 4 ALA A 154 GLY A 159 1 O ALA A 158 N VAL A 74 SHEET 4 AA1 4 VAL A 178 ASN A 182 1 O ILE A 179 N VAL A 155 SHEET 1 AA2 2 ARG A 215 ARG A 219 0 SHEET 2 AA2 2 LEU A 435 LEU A 439 -1 O THR A 437 N LEU A 217 SHEET 1 AA3 6 SER A 265 ALA A 274 0 SHEET 2 AA3 6 ILE A 222 GLY A 228 -1 N LEU A 224 O LEU A 270 SHEET 3 AA3 6 ALA A 423 ILE A 429 -1 O ILE A 424 N GLU A 227 SHEET 4 AA3 6 LYS A 397 SER A 402 -1 N SER A 402 O ALA A 423 SHEET 5 AA3 6 SER A 289 VAL A 295 -1 N SER A 294 O CYS A 399 SHEET 6 AA3 6 GLU A 301 SER A 305 -1 O SER A 305 N SER A 289 SHEET 1 AA4 7 VAL A 236 ASP A 237 0 SHEET 2 AA4 7 THR A 415 GLU A 418 -1 O SER A 416 N VAL A 236 SHEET 3 AA4 7 ALA A 407 VAL A 411 -1 N VAL A 411 O THR A 415 SHEET 4 AA4 7 GLU A 277 GLU A 282 -1 N PHE A 279 O VAL A 410 SHEET 5 AA4 7 LEU A 308 CYS A 311 -1 O LEU A 308 N ILE A 280 SHEET 6 AA4 7 ILE A 373 ILE A 377 -1 O SER A 376 N ASN A 309 SHEET 7 AA4 7 ARG A 392 SER A 395 -1 O SER A 395 N ILE A 373 LINK O1A NAP A 501 CA CA A 502 1555 1555 2.33 LINK O1N NAP A 501 CA CA A 502 1555 1555 2.38 LINK O3X NAP A 501 CA CA A 502 1555 1555 2.41 LINK CA CA A 502 O HOH A 721 1555 1555 2.79 LINK CA CA A 502 O HOH A 726 1555 1555 2.45 LINK CA CA A 502 O HOH A 728 1555 1555 2.40 CRYST1 68.470 68.470 223.420 90.00 90.00 90.00 P 43 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 0.014605 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004476 0.00000 CONECT 2670 2671 2672 2673 2692 CONECT 2671 2670 2718 CONECT 2672 2670 CONECT 2673 2670 2674 CONECT 2674 2673 2675 CONECT 2675 2674 2676 2677 CONECT 2676 2675 2681 CONECT 2677 2675 2678 2679 CONECT 2678 2677 CONECT 2679 2677 2680 2681 CONECT 2680 2679 2714 CONECT 2681 2676 2679 2682 CONECT 2682 2681 2683 2691 CONECT 2683 2682 2684 CONECT 2684 2683 2685 CONECT 2685 2684 2686 2691 CONECT 2686 2685 2687 2688 CONECT 2687 2686 CONECT 2688 2686 2689 CONECT 2689 2688 2690 CONECT 2690 2689 2691 CONECT 2691 2682 2685 2690 CONECT 2692 2670 2693 CONECT 2693 2692 2694 2695 2696 CONECT 2694 2693 2718 CONECT 2695 2693 CONECT 2696 2693 2697 CONECT 2697 2696 2698 CONECT 2698 2697 2699 2700 CONECT 2699 2698 2704 CONECT 2700 2698 2701 2702 CONECT 2701 2700 CONECT 2702 2700 2703 2704 CONECT 2703 2702 CONECT 2704 2699 2702 2705 CONECT 2705 2704 2706 2713 CONECT 2706 2705 2707 CONECT 2707 2706 2708 2711 CONECT 2708 2707 2709 2710 CONECT 2709 2708 CONECT 2710 2708 CONECT 2711 2707 2712 CONECT 2712 2711 2713 CONECT 2713 2705 2712 CONECT 2714 2680 2715 2716 2717 CONECT 2715 2714 CONECT 2716 2714 CONECT 2717 2714 2718 CONECT 2718 2671 2694 2717 2839 CONECT 2718 2844 2846 CONECT 2839 2718 CONECT 2844 2718 CONECT 2846 2718 MASTER 469 0 2 12 19 0 0 6 2854 1 53 31 END