HEADER TRANSFERASE 08-FEB-22 7R4K TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL NAD KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD KINASE 2, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: MITOCHONDRIAL NAD KINASE,NAD KINASE DOMAIN-CONTAINING COMPND 6 PROTEIN 1,MITOCHONDRIAL; COMPND 7 EC: 2.7.1.23; COMPND 8 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 NADP BOUND FORM WITH MAGNESIUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.LABESSE,C.MARY,M.GELIN,C.LIONNE REVDAT 4 01-MAY-24 7R4K 1 REMARK REVDAT 3 14-SEP-22 7R4K 1 JRNL REVDAT 2 03-AUG-22 7R4K 1 JRNL REVDAT 1 06-JUL-22 7R4K 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. 3.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1-4122 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) : 3.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 12876 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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 37.0900 - 5.6900 0.88 2415 125 0.1871 0.2618 REMARK 3 2 5.6900 - 4.5200 0.90 2455 130 0.1937 0.2583 REMARK 3 3 4.5200 - 3.9500 0.90 2431 129 0.2100 0.2967 REMARK 3 4 3.9500 - 3.5900 0.90 2452 135 0.2393 0.3142 REMARK 3 5 3.5900 - 3.3300 0.90 2478 126 0.2950 0.3525 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 78.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.77 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.2773 -6.7222 29.3322 REMARK 3 T TENSOR REMARK 3 T11: 0.5944 T22: 0.5315 REMARK 3 T33: 0.5174 T12: -0.1362 REMARK 3 T13: 0.0102 T23: -0.1834 REMARK 3 L TENSOR REMARK 3 L11: 8.5038 L22: 6.4131 REMARK 3 L33: 3.4695 L12: -1.6137 REMARK 3 L13: -1.8209 L23: 1.5065 REMARK 3 S TENSOR REMARK 3 S11: 0.5935 S12: -0.3315 S13: 0.8222 REMARK 3 S21: -0.4118 S22: -0.1718 S23: 0.4376 REMARK 3 S31: -1.1186 S32: -0.2783 S33: -0.2660 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 133 THROUGH 282 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3911 -20.0026 25.0008 REMARK 3 T TENSOR REMARK 3 T11: 0.3370 T22: 0.4639 REMARK 3 T33: 0.5938 T12: -0.0111 REMARK 3 T13: -0.0357 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 3.4914 L22: 1.3856 REMARK 3 L33: 5.1895 L12: -2.0791 REMARK 3 L13: -2.4108 L23: 1.9440 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.4238 S13: 0.0391 REMARK 3 S21: 0.0040 S22: 0.1097 S23: -0.1189 REMARK 3 S31: 0.1473 S32: 0.4476 S33: -0.1062 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 283 THROUGH 377 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.6900 -33.0863 4.9862 REMARK 3 T TENSOR REMARK 3 T11: 0.5481 T22: 0.4107 REMARK 3 T33: 0.6328 T12: -0.0777 REMARK 3 T13: -0.0748 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 3.7469 L22: 3.5082 REMARK 3 L33: 5.4187 L12: 0.0678 REMARK 3 L13: -0.1366 L23: -0.5738 REMARK 3 S TENSOR REMARK 3 S11: -0.3294 S12: 0.1396 S13: -0.1293 REMARK 3 S21: -0.1485 S22: 0.2296 S23: 0.7334 REMARK 3 S31: 0.4193 S32: -0.7818 S33: -0.0133 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 378 THROUGH 441 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0837 -29.7497 8.1603 REMARK 3 T TENSOR REMARK 3 T11: 0.3781 T22: 0.5214 REMARK 3 T33: 0.5562 T12: 0.0037 REMARK 3 T13: -0.0792 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 4.6484 L22: 3.0054 REMARK 3 L33: 7.7396 L12: -0.1555 REMARK 3 L13: -0.6443 L23: 0.4653 REMARK 3 S TENSOR REMARK 3 S11: -0.0709 S12: 0.9633 S13: -0.3122 REMARK 3 S21: -0.3758 S22: 0.0105 S23: -0.1368 REMARK 3 S31: 0.7914 S32: 0.8380 S33: -0.0802 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 7R4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120910. 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18108 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 37.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 3.379 REMARK 200 R MERGE (I) : 0.27600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.13 REMARK 200 R MERGE FOR SHELL (I) : 2.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.680 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 (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 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 110.90750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.79150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.79150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 166.36125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.79150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.79150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.45375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.79150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.79150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 166.36125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.79150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.79150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.45375 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 110.90750 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: 6840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 653 LIES ON A SPECIAL POSITION. 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 LEU A 103 REMARK 465 LYS A 104 REMARK 465 GLY A 105 REMARK 465 SER A 106 REMARK 465 SER A 107 REMARK 465 TYR A 108 REMARK 465 SER A 109 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 465 GLY A 342 REMARK 465 ASN A 343 REMARK 465 LEU A 344 REMARK 465 SER A 345 REMARK 465 GLN A 442 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 340 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 341 CG CD OE1 NE2 REMARK 470 LEU A 346 CG CD1 CD2 REMARK 470 LEU A 348 CG CD1 CD2 REMARK 470 ASN A 349 CG OD1 ND2 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 SER A 169 O HOH A 601 2.08 REMARK 500 OE2 GLU A 370 O HOH A 602 2.08 REMARK 500 O ARG A 221 O HOH A 603 2.10 REMARK 500 OH TYR A 360 NH2 ARG A 392 2.19 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 PHE A 66 122.02 174.91 REMARK 500 LYS A 120 -3.45 -59.70 REMARK 500 LYS A 140 -160.11 -119.18 REMARK 500 ARG A 141 -76.54 -45.78 REMARK 500 TYR A 144 74.85 -62.20 REMARK 500 LYS A 170 33.32 -90.00 REMARK 500 ARG A 174 5.25 -69.54 REMARK 500 ASN A 182 101.84 -52.76 REMARK 500 ASP A 184 62.47 -150.78 REMARK 500 HIS A 239 39.32 -78.96 REMARK 500 ALA A 318 -118.07 -77.87 REMARK 500 ASN A 349 -168.32 -123.74 REMARK 500 SER A 363 8.81 -64.72 REMARK 500 PRO A 371 46.55 -102.45 REMARK 500 GLU A 379 75.07 56.06 REMARK 500 ALA A 382 -132.58 -74.57 REMARK 500 ASN A 383 -169.22 72.85 REMARK 500 PHE A 386 70.63 -118.99 REMARK 500 SER A 389 -126.24 -81.80 REMARK 500 ASP A 406 72.44 -152.21 REMARK 500 ASN A 420 -169.50 -111.15 REMARK 500 GLU A 432 14.81 -66.35 REMARK 500 VAL A 438 -163.69 -112.51 REMARK 500 LEU A 439 113.99 -175.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 67 0.10 SIDE CHAIN 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 A 678 DISTANCE = 5.83 ANGSTROMS 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 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAP A 501 O1A REMARK 620 2 NAP A 501 O3X 72.8 REMARK 620 3 HOH A 606 O 80.0 78.6 REMARK 620 4 HOH A 611 O 130.7 59.2 100.0 REMARK 620 5 HOH A 632 O 75.9 146.9 85.7 153.4 REMARK 620 N 1 2 3 4 DBREF 7R4K A 61 442 UNP Q4G0N4 NAKD2_HUMAN 61 442 SEQADV 7R4K MET A 52 UNP Q4G0N4 INITIATING METHIONINE SEQADV 7R4K GLY A 53 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4K HIS A 54 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4K HIS A 55 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4K HIS A 56 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4K HIS A 57 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4K HIS A 58 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4K HIS A 59 UNP Q4G0N4 EXPRESSION TAG SEQADV 7R4K 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 MG A 502 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM MG MAGNESIUM ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *78(H2 O) HELIX 1 AA1 THR A 78 GLN A 85 1 8 HELIX 2 AA2 LEU A 111 ASN A 131 1 21 HELIX 3 AA3 ASP A 145 ALA A 152 1 8 HELIX 4 AA4 GLY A 160 LYS A 170 1 11 HELIX 5 AA5 PRO A 195 HIS A 200 5 6 HELIX 6 AA6 SER A 201 ARG A 211 1 11 HELIX 7 AA7 ALA A 318 ARG A 325 1 8 HELIX 8 AA8 ALA A 327 GLN A 341 1 15 HELIX 9 AA9 ASN A 349 SER A 363 1 15 HELIX 10 AB1 LYS A 431 GLU A 434 5 4 SHEET 1 AA1 4 GLU A 135 VAL A 139 0 SHEET 2 AA1 4 ARG A 70 ALA A 75 1 N VAL A 73 O ARG A 137 SHEET 3 AA1 4 ALA A 154 GLY A 159 1 O ILE A 156 N VAL A 74 SHEET 4 AA1 4 VAL A 178 ASN A 182 1 O VAL A 181 N ALA A 157 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 LEU A 269 0 SHEET 2 AA3 6 ILE A 222 GLY A 228 -1 N LEU A 226 O GLN A 268 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 VAL A 400 O ALA A 425 SHEET 5 AA3 6 SER A 289 VAL A 295 -1 N GLU A 292 O ARG A 401 SHEET 6 AA3 6 GLU A 301 SER A 305 -1 O SER A 305 N SER A 289 SHEET 1 AA4 5 ASN A 232 ASP A 237 0 SHEET 2 AA4 5 THR A 415 GLU A 418 -1 O SER A 416 N VAL A 236 SHEET 3 AA4 5 ALA A 407 VAL A 411 -1 N MET A 409 O PHE A 417 SHEET 4 AA4 5 GLU A 277 GLU A 282 -1 N PHE A 279 O VAL A 410 SHEET 5 AA4 5 LEU A 308 CYS A 311 -1 O LEU A 308 N ILE A 280 SHEET 1 AA5 2 ILE A 373 SER A 376 0 SHEET 2 AA5 2 ARG A 392 SER A 395 -1 O SER A 395 N ILE A 373 LINK O1A NAP A 501 MG MG A 502 1555 1555 2.15 LINK O3X NAP A 501 MG MG A 502 1555 1555 2.69 LINK MG MG A 502 O HOH A 606 1555 1555 2.77 LINK MG MG A 502 O HOH A 611 1555 1555 2.20 LINK MG MG A 502 O HOH A 632 1555 1555 2.53 CRYST1 67.583 67.583 221.815 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 0.014797 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014797 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004508 0.00000 CONECT 2580 2581 2582 2583 2602 CONECT 2581 2580 2628 CONECT 2582 2580 CONECT 2583 2580 2584 CONECT 2584 2583 2585 CONECT 2585 2584 2586 2587 CONECT 2586 2585 2591 CONECT 2587 2585 2588 2589 CONECT 2588 2587 CONECT 2589 2587 2590 2591 CONECT 2590 2589 2624 CONECT 2591 2586 2589 2592 CONECT 2592 2591 2593 2601 CONECT 2593 2592 2594 CONECT 2594 2593 2595 CONECT 2595 2594 2596 2601 CONECT 2596 2595 2597 2598 CONECT 2597 2596 CONECT 2598 2596 2599 CONECT 2599 2598 2600 CONECT 2600 2599 2601 CONECT 2601 2592 2595 2600 CONECT 2602 2580 2603 CONECT 2603 2602 2604 2605 2606 CONECT 2604 2603 CONECT 2605 2603 CONECT 2606 2603 2607 CONECT 2607 2606 2608 CONECT 2608 2607 2609 2610 CONECT 2609 2608 2614 CONECT 2610 2608 2611 2612 CONECT 2611 2610 CONECT 2612 2610 2613 2614 CONECT 2613 2612 CONECT 2614 2609 2612 2615 CONECT 2615 2614 2616 2623 CONECT 2616 2615 2617 CONECT 2617 2616 2618 2621 CONECT 2618 2617 2619 2620 CONECT 2619 2618 CONECT 2620 2618 CONECT 2621 2617 2622 CONECT 2622 2621 2623 CONECT 2623 2615 2622 CONECT 2624 2590 2625 2626 2627 CONECT 2625 2624 CONECT 2626 2624 CONECT 2627 2624 2628 CONECT 2628 2581 2627 2634 2639 CONECT 2628 2660 CONECT 2634 2628 CONECT 2639 2628 CONECT 2660 2628 MASTER 467 0 2 10 19 0 0 6 2705 1 53 31 END