HEADER TRANSFERASE 15-APR-22 7ZLW TITLE NME1 IN COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE A; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: NDK A,NDP KINASE A,METASTASIS INHIBITION FACTOR NM23,NDPK-A, COMPND 5 TUMOR METASTATIC PROCESS-ASSOCIATED PROTEIN,NM23-M1; COMPND 6 EC: 2.7.4.6; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: THE CHAIN E OF HEXAMERIC NME1 DOES NOT HAVE ADP BOUND. COMPND 9 SOME RESIDUES AROUND THE NUCLEOTIDE BINDING REGION ARE DISORDERED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NME1, NM23; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS NME1, COMPLEX, TRANSFERASE, NUCLEOSIDE DIPHOSPHATE KINASE 1, ADP EXPDTA X-RAY DIFFRACTION AUTHOR I.GARCIA-SAEZ,D.IUSO,S.KHOCHBIN,C.PETOSA REVDAT 3 16-OCT-24 7ZLW 1 REMARK REVDAT 2 20-SEP-23 7ZLW 1 JRNL REVDAT 1 09-AUG-23 7ZLW 0 JRNL AUTH D.IUSO,I.GARCIA-SAEZ,Y.COUTE,Y.YAMARYO-BOTTE,E.BOERI ERBA, JRNL AUTH 2 A.ADRAIT,N.ZEAITER,M.TOKARSKA-SCHLATTNER,Z.M.JILKOVA, JRNL AUTH 3 F.BOUSSOUAR,S.BARRAL,L.SIGNOR,K.COUTURIER,A.HAJMIRZA, JRNL AUTH 4 F.CHUFFART,E.BOUROVA-FLIN,A.L.VITTE,L.BARGIER,D.PUTHIER, JRNL AUTH 5 T.DECAENS,S.ROUSSEAUX,C.BOTTE,U.SCHLATTNER,C.PETOSA, JRNL AUTH 6 S.KHOCHBIN JRNL TITL NUCLEOSIDE DIPHOSPHATE KINASES 1 AND 2 REGULATE A PROTECTIVE JRNL TITL 2 LIVER RESPONSE TO A HIGH-FAT DIET. JRNL REF SCI ADV V. 9 H0140 2023 JRNL REFN ESSN 2375-2548 JRNL PMID 37672589 JRNL DOI 10.1126/SCIADV.ADH0140 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 39106 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 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 59.6500 - 5.3000 0.95 2738 159 0.1620 0.1880 REMARK 3 2 5.3000 - 4.2100 0.97 2739 146 0.1358 0.1504 REMARK 3 3 4.2100 - 3.6800 0.98 2722 147 0.1367 0.2195 REMARK 3 4 3.6800 - 3.3400 0.97 2691 168 0.1556 0.1845 REMARK 3 5 3.3400 - 3.1000 0.97 2759 123 0.1676 0.2333 REMARK 3 6 3.1000 - 2.9200 0.98 2729 151 0.1826 0.2534 REMARK 3 7 2.9200 - 2.7700 0.99 2742 181 0.1961 0.2641 REMARK 3 8 2.7700 - 2.6500 0.99 2749 144 0.2023 0.2527 REMARK 3 9 2.6500 - 2.5500 0.99 2775 135 0.1948 0.2500 REMARK 3 10 2.5500 - 2.4600 0.99 2746 143 0.2105 0.2743 REMARK 3 11 2.4600 - 2.3800 0.99 2811 126 0.2130 0.2801 REMARK 3 12 2.3800 - 2.3200 0.95 2622 154 0.2069 0.2501 REMARK 3 13 2.3200 - 2.2600 0.82 2250 129 0.2301 0.3024 REMARK 3 14 2.2600 - 2.2000 0.72 2041 86 0.2259 0.3184 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.04 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 201) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0947 10.1804 103.3476 REMARK 3 T TENSOR REMARK 3 T11: 0.1788 T22: 0.1192 REMARK 3 T33: 0.1734 T12: 0.0075 REMARK 3 T13: -0.0192 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 0.9463 L22: 0.8031 REMARK 3 L33: 1.0076 L12: -0.1076 REMARK 3 L13: -0.0745 L23: -0.3416 REMARK 3 S TENSOR REMARK 3 S11: -0.0554 S12: -0.0985 S13: -0.1029 REMARK 3 S21: 0.1361 S22: 0.0499 S23: -0.1521 REMARK 3 S31: 0.1273 S32: -0.0079 S33: 0.0040 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 0 THROUGH 201) REMARK 3 ORIGIN FOR THE GROUP (A): 22.7960 36.5668 83.4394 REMARK 3 T TENSOR REMARK 3 T11: 0.2764 T22: 0.1000 REMARK 3 T33: 0.2127 T12: 0.0032 REMARK 3 T13: -0.0229 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 0.6184 L22: 0.8382 REMARK 3 L33: 0.7692 L12: -0.0308 REMARK 3 L13: 0.1495 L23: -0.1131 REMARK 3 S TENSOR REMARK 3 S11: -0.0833 S12: 0.0561 S13: 0.1792 REMARK 3 S21: 0.0875 S22: -0.0047 S23: -0.1208 REMARK 3 S31: -0.3474 S32: -0.0185 S33: 0.0194 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 201) REMARK 3 ORIGIN FOR THE GROUP (A): 25.8263 6.3101 70.3612 REMARK 3 T TENSOR REMARK 3 T11: 0.2378 T22: 0.1741 REMARK 3 T33: 0.2299 T12: -0.0021 REMARK 3 T13: 0.0620 T23: -0.0443 REMARK 3 L TENSOR REMARK 3 L11: 0.8355 L22: 0.7485 REMARK 3 L33: 1.1668 L12: 0.3110 REMARK 3 L13: -0.1687 L23: 0.3222 REMARK 3 S TENSOR REMARK 3 S11: -0.0214 S12: 0.2151 S13: -0.1657 REMARK 3 S21: -0.1627 S22: -0.0304 S23: -0.2214 REMARK 3 S31: 0.2496 S32: 0.0144 S33: 0.0131 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 2 THROUGH 201) REMARK 3 ORIGIN FOR THE GROUP (A): -0.0670 4.4315 100.2721 REMARK 3 T TENSOR REMARK 3 T11: 0.0903 T22: 0.4931 REMARK 3 T33: 0.1898 T12: -0.3201 REMARK 3 T13: 0.1687 T23: 0.1299 REMARK 3 L TENSOR REMARK 3 L11: 0.8973 L22: 0.4427 REMARK 3 L33: 1.2183 L12: -0.2264 REMARK 3 L13: -0.0682 L23: -0.2607 REMARK 3 S TENSOR REMARK 3 S11: -0.3179 S12: -0.3045 S13: -0.0664 REMARK 3 S21: 0.2133 S22: 0.1978 S23: 0.1711 REMARK 3 S31: 0.1472 S32: -0.9859 S33: 0.0151 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN 'E' AND RESID 1 THROUGH 152) REMARK 3 ORIGIN FOR THE GROUP (A): -0.4391 34.0856 83.6386 REMARK 3 T TENSOR REMARK 3 T11: 0.2129 T22: 0.4129 REMARK 3 T33: 0.2493 T12: 0.1884 REMARK 3 T13: -0.0073 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 1.2336 L22: 1.4274 REMARK 3 L33: 1.1312 L12: 0.1258 REMARK 3 L13: 0.4476 L23: -0.3956 REMARK 3 S TENSOR REMARK 3 S11: -0.0168 S12: 0.0868 S13: 0.1898 REMARK 3 S21: 0.1324 S22: 0.0471 S23: 0.2054 REMARK 3 S31: -0.3001 S32: -0.4900 S33: -0.0081 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN 'F' AND RESID 1 THROUGH 201) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3532 6.9514 67.4570 REMARK 3 T TENSOR REMARK 3 T11: 0.2238 T22: 0.4962 REMARK 3 T33: 0.2299 T12: -0.1213 REMARK 3 T13: -0.0679 T23: -0.1355 REMARK 3 L TENSOR REMARK 3 L11: 0.8471 L22: 0.6643 REMARK 3 L33: 0.9681 L12: 0.0664 REMARK 3 L13: -0.0609 L23: 0.2357 REMARK 3 S TENSOR REMARK 3 S11: 0.0807 S12: 0.2555 S13: -0.1730 REMARK 3 S21: -0.0860 S22: -0.1519 S23: 0.1520 REMARK 3 S31: 0.2683 S32: -0.5517 S33: -0.0103 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 7ZLW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122461. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.966000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN 26, 2018 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40517 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 59.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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: 2HVD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, NACL, TRIS, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 35.09650 REMARK 290 SMTRY3 2 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 GLY B -3 REMARK 465 ALA B -2 REMARK 465 MET B -1 REMARK 465 GLY C -3 REMARK 465 ALA C -2 REMARK 465 MET C -1 REMARK 465 ALA C 0 REMARK 465 GLY D -3 REMARK 465 ALA D -2 REMARK 465 MET D -1 REMARK 465 ALA D 0 REMARK 465 MET D 1 REMARK 465 TRP D 149 REMARK 465 ILE D 150 REMARK 465 TYR D 151 REMARK 465 GLU D 152 REMARK 465 GLY E -3 REMARK 465 ALA E -2 REMARK 465 MET E -1 REMARK 465 ALA E 0 REMARK 465 TYR E 52 REMARK 465 THR E 53 REMARK 465 ASP E 54 REMARK 465 LEU E 55 REMARK 465 LYS E 56 REMARK 465 ASP E 57 REMARK 465 ARG E 58 REMARK 465 PRO E 59 REMARK 465 PHE E 60 REMARK 465 PHE E 61 REMARK 465 THR E 62 REMARK 465 GLY E 63 REMARK 465 LEU E 64 REMARK 465 GLY F -3 REMARK 465 ALA F -2 REMARK 465 MET F -1 REMARK 465 ALA F 0 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 C 67 O HOH C 301 2.10 REMARK 500 O2B ADP A 201 O HOH A 301 2.15 REMARK 500 O HOH A 301 O HOH A 371 2.16 REMARK 500 O SER E 131 O HOH E 201 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 ILE A 110 -45.73 -130.70 REMARK 500 ILE A 116 -20.14 53.00 REMARK 500 ALA A 146 69.64 -66.40 REMARK 500 GLN A 147 -22.03 -143.59 REMARK 500 LEU B 38 119.54 -160.40 REMARK 500 ILE B 116 -20.34 55.14 REMARK 500 ILE C 110 -51.38 -121.44 REMARK 500 ILE C 116 -17.87 52.39 REMARK 500 TYR D 52 44.84 -106.56 REMARK 500 ILE D 110 -53.64 -128.36 REMARK 500 ILE D 116 -29.06 54.09 REMARK 500 ALA D 146 -123.25 55.88 REMARK 500 ALA D 146 -123.25 64.22 REMARK 500 GLN D 147 -107.76 46.68 REMARK 500 ALA E 2 -80.41 59.47 REMARK 500 ASP E 46 7.01 -68.37 REMARK 500 ILE F 110 -51.67 -122.09 REMARK 500 ILE F 116 -25.22 52.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 394 DISTANCE = 6.59 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ZL8 RELATED DB: PDB REMARK 900 7ZL8 CONTAINS THE SAME PROTEIN IN COMPLEX WITH SUCCINYL-COA DBREF 7ZLW A 1 152 UNP P15532 NDKA_MOUSE 1 152 DBREF 7ZLW B 1 152 UNP P15532 NDKA_MOUSE 1 152 DBREF 7ZLW C 1 152 UNP P15532 NDKA_MOUSE 1 152 DBREF 7ZLW D 1 152 UNP P15532 NDKA_MOUSE 1 152 DBREF 7ZLW E 1 152 UNP P15532 NDKA_MOUSE 1 152 DBREF 7ZLW F 1 152 UNP P15532 NDKA_MOUSE 1 152 SEQADV 7ZLW GLY A -3 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA A -2 UNP P15532 EXPRESSION TAG SEQADV 7ZLW MET A -1 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA A 0 UNP P15532 EXPRESSION TAG SEQADV 7ZLW GLY B -3 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA B -2 UNP P15532 EXPRESSION TAG SEQADV 7ZLW MET B -1 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA B 0 UNP P15532 EXPRESSION TAG SEQADV 7ZLW GLY C -3 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA C -2 UNP P15532 EXPRESSION TAG SEQADV 7ZLW MET C -1 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA C 0 UNP P15532 EXPRESSION TAG SEQADV 7ZLW GLY D -3 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA D -2 UNP P15532 EXPRESSION TAG SEQADV 7ZLW MET D -1 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA D 0 UNP P15532 EXPRESSION TAG SEQADV 7ZLW GLY E -3 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA E -2 UNP P15532 EXPRESSION TAG SEQADV 7ZLW MET E -1 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA E 0 UNP P15532 EXPRESSION TAG SEQADV 7ZLW GLY F -3 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA F -2 UNP P15532 EXPRESSION TAG SEQADV 7ZLW MET F -1 UNP P15532 EXPRESSION TAG SEQADV 7ZLW ALA F 0 UNP P15532 EXPRESSION TAG SEQRES 1 A 156 GLY ALA MET ALA MET ALA ASN SER GLU ARG THR PHE ILE SEQRES 2 A 156 ALA ILE LYS PRO ASP GLY VAL GLN ARG GLY LEU VAL GLY SEQRES 3 A 156 GLU ILE ILE LYS ARG PHE GLU GLN LYS GLY PHE ARG LEU SEQRES 4 A 156 VAL GLY LEU LYS PHE LEU GLN ALA SER GLU ASP LEU LEU SEQRES 5 A 156 LYS GLU HIS TYR THR ASP LEU LYS ASP ARG PRO PHE PHE SEQRES 6 A 156 THR GLY LEU VAL LYS TYR MET HIS SER GLY PRO VAL VAL SEQRES 7 A 156 ALA MET VAL TRP GLU GLY LEU ASN VAL VAL LYS THR GLY SEQRES 8 A 156 ARG VAL MET LEU GLY GLU THR ASN PRO ALA ASP SER LYS SEQRES 9 A 156 PRO GLY THR ILE ARG GLY ASP PHE CYS ILE GLN VAL GLY SEQRES 10 A 156 ARG ASN ILE ILE HIS GLY SER ASP SER VAL LYS SER ALA SEQRES 11 A 156 GLU LYS GLU ILE SER LEU TRP PHE GLN PRO GLU GLU LEU SEQRES 12 A 156 VAL GLU TYR LYS SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 B 156 GLY ALA MET ALA MET ALA ASN SER GLU ARG THR PHE ILE SEQRES 2 B 156 ALA ILE LYS PRO ASP GLY VAL GLN ARG GLY LEU VAL GLY SEQRES 3 B 156 GLU ILE ILE LYS ARG PHE GLU GLN LYS GLY PHE ARG LEU SEQRES 4 B 156 VAL GLY LEU LYS PHE LEU GLN ALA SER GLU ASP LEU LEU SEQRES 5 B 156 LYS GLU HIS TYR THR ASP LEU LYS ASP ARG PRO PHE PHE SEQRES 6 B 156 THR GLY LEU VAL LYS TYR MET HIS SER GLY PRO VAL VAL SEQRES 7 B 156 ALA MET VAL TRP GLU GLY LEU ASN VAL VAL LYS THR GLY SEQRES 8 B 156 ARG VAL MET LEU GLY GLU THR ASN PRO ALA ASP SER LYS SEQRES 9 B 156 PRO GLY THR ILE ARG GLY ASP PHE CYS ILE GLN VAL GLY SEQRES 10 B 156 ARG ASN ILE ILE HIS GLY SER ASP SER VAL LYS SER ALA SEQRES 11 B 156 GLU LYS GLU ILE SER LEU TRP PHE GLN PRO GLU GLU LEU SEQRES 12 B 156 VAL GLU TYR LYS SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 C 156 GLY ALA MET ALA MET ALA ASN SER GLU ARG THR PHE ILE SEQRES 2 C 156 ALA ILE LYS PRO ASP GLY VAL GLN ARG GLY LEU VAL GLY SEQRES 3 C 156 GLU ILE ILE LYS ARG PHE GLU GLN LYS GLY PHE ARG LEU SEQRES 4 C 156 VAL GLY LEU LYS PHE LEU GLN ALA SER GLU ASP LEU LEU SEQRES 5 C 156 LYS GLU HIS TYR THR ASP LEU LYS ASP ARG PRO PHE PHE SEQRES 6 C 156 THR GLY LEU VAL LYS TYR MET HIS SER GLY PRO VAL VAL SEQRES 7 C 156 ALA MET VAL TRP GLU GLY LEU ASN VAL VAL LYS THR GLY SEQRES 8 C 156 ARG VAL MET LEU GLY GLU THR ASN PRO ALA ASP SER LYS SEQRES 9 C 156 PRO GLY THR ILE ARG GLY ASP PHE CYS ILE GLN VAL GLY SEQRES 10 C 156 ARG ASN ILE ILE HIS GLY SER ASP SER VAL LYS SER ALA SEQRES 11 C 156 GLU LYS GLU ILE SER LEU TRP PHE GLN PRO GLU GLU LEU SEQRES 12 C 156 VAL GLU TYR LYS SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 D 156 GLY ALA MET ALA MET ALA ASN SER GLU ARG THR PHE ILE SEQRES 2 D 156 ALA ILE LYS PRO ASP GLY VAL GLN ARG GLY LEU VAL GLY SEQRES 3 D 156 GLU ILE ILE LYS ARG PHE GLU GLN LYS GLY PHE ARG LEU SEQRES 4 D 156 VAL GLY LEU LYS PHE LEU GLN ALA SER GLU ASP LEU LEU SEQRES 5 D 156 LYS GLU HIS TYR THR ASP LEU LYS ASP ARG PRO PHE PHE SEQRES 6 D 156 THR GLY LEU VAL LYS TYR MET HIS SER GLY PRO VAL VAL SEQRES 7 D 156 ALA MET VAL TRP GLU GLY LEU ASN VAL VAL LYS THR GLY SEQRES 8 D 156 ARG VAL MET LEU GLY GLU THR ASN PRO ALA ASP SER LYS SEQRES 9 D 156 PRO GLY THR ILE ARG GLY ASP PHE CYS ILE GLN VAL GLY SEQRES 10 D 156 ARG ASN ILE ILE HIS GLY SER ASP SER VAL LYS SER ALA SEQRES 11 D 156 GLU LYS GLU ILE SER LEU TRP PHE GLN PRO GLU GLU LEU SEQRES 12 D 156 VAL GLU TYR LYS SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 E 156 GLY ALA MET ALA MET ALA ASN SER GLU ARG THR PHE ILE SEQRES 2 E 156 ALA ILE LYS PRO ASP GLY VAL GLN ARG GLY LEU VAL GLY SEQRES 3 E 156 GLU ILE ILE LYS ARG PHE GLU GLN LYS GLY PHE ARG LEU SEQRES 4 E 156 VAL GLY LEU LYS PHE LEU GLN ALA SER GLU ASP LEU LEU SEQRES 5 E 156 LYS GLU HIS TYR THR ASP LEU LYS ASP ARG PRO PHE PHE SEQRES 6 E 156 THR GLY LEU VAL LYS TYR MET HIS SER GLY PRO VAL VAL SEQRES 7 E 156 ALA MET VAL TRP GLU GLY LEU ASN VAL VAL LYS THR GLY SEQRES 8 E 156 ARG VAL MET LEU GLY GLU THR ASN PRO ALA ASP SER LYS SEQRES 9 E 156 PRO GLY THR ILE ARG GLY ASP PHE CYS ILE GLN VAL GLY SEQRES 10 E 156 ARG ASN ILE ILE HIS GLY SER ASP SER VAL LYS SER ALA SEQRES 11 E 156 GLU LYS GLU ILE SER LEU TRP PHE GLN PRO GLU GLU LEU SEQRES 12 E 156 VAL GLU TYR LYS SER CYS ALA GLN ASN TRP ILE TYR GLU SEQRES 1 F 156 GLY ALA MET ALA MET ALA ASN SER GLU ARG THR PHE ILE SEQRES 2 F 156 ALA ILE LYS PRO ASP GLY VAL GLN ARG GLY LEU VAL GLY SEQRES 3 F 156 GLU ILE ILE LYS ARG PHE GLU GLN LYS GLY PHE ARG LEU SEQRES 4 F 156 VAL GLY LEU LYS PHE LEU GLN ALA SER GLU ASP LEU LEU SEQRES 5 F 156 LYS GLU HIS TYR THR ASP LEU LYS ASP ARG PRO PHE PHE SEQRES 6 F 156 THR GLY LEU VAL LYS TYR MET HIS SER GLY PRO VAL VAL SEQRES 7 F 156 ALA MET VAL TRP GLU GLY LEU ASN VAL VAL LYS THR GLY SEQRES 8 F 156 ARG VAL MET LEU GLY GLU THR ASN PRO ALA ASP SER LYS SEQRES 9 F 156 PRO GLY THR ILE ARG GLY ASP PHE CYS ILE GLN VAL GLY SEQRES 10 F 156 ARG ASN ILE ILE HIS GLY SER ASP SER VAL LYS SER ALA SEQRES 11 F 156 GLU LYS GLU ILE SER LEU TRP PHE GLN PRO GLU GLU LEU SEQRES 12 F 156 VAL GLU TYR LYS SER CYS ALA GLN ASN TRP ILE TYR GLU HET ADP A 201 27 HET ADP B 201 27 HET ADP C 201 27 HET ADP D 201 27 HET ADP F 201 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 7 ADP 5(C10 H15 N5 O10 P2) FORMUL 12 HOH *452(H2 O) HELIX 1 AA1 MET A 1 SER A 4 5 4 HELIX 2 AA2 LYS A 12 ARG A 18 1 7 HELIX 3 AA3 LEU A 20 GLY A 32 1 13 HELIX 4 AA4 SER A 44 TYR A 52 1 9 HELIX 5 AA5 THR A 53 LYS A 56 5 4 HELIX 6 AA6 PHE A 60 SER A 70 1 11 HELIX 7 AA7 ASN A 82 GLY A 92 1 11 HELIX 8 AA8 ASN A 95 SER A 99 5 5 HELIX 9 AA9 THR A 103 CYS A 109 1 7 HELIX 10 AB1 GLN A 111 ASN A 115 5 5 HELIX 11 AB2 SER A 122 PHE A 134 1 13 HELIX 12 AB3 GLN A 135 LEU A 139 5 5 HELIX 13 AB4 MET B 1 SER B 4 5 4 HELIX 14 AB5 LYS B 12 ARG B 18 1 7 HELIX 15 AB6 LEU B 20 GLY B 32 1 13 HELIX 16 AB7 SER B 44 TYR B 52 1 9 HELIX 17 AB8 THR B 53 LYS B 56 5 4 HELIX 18 AB9 PHE B 60 SER B 70 1 11 HELIX 19 AC1 ASN B 82 GLY B 92 1 11 HELIX 20 AC2 ASN B 95 SER B 99 5 5 HELIX 21 AC3 THR B 103 CYS B 109 1 7 HELIX 22 AC4 GLN B 111 ASN B 115 5 5 HELIX 23 AC5 SER B 122 PHE B 134 1 13 HELIX 24 AC6 GLN B 135 LEU B 139 5 5 HELIX 25 AC7 ALA B 146 TYR B 151 1 6 HELIX 26 AC8 MET C 1 SER C 4 5 4 HELIX 27 AC9 LYS C 12 ARG C 18 1 7 HELIX 28 AD1 LEU C 20 GLY C 32 1 13 HELIX 29 AD2 SER C 44 TYR C 52 1 9 HELIX 30 AD3 THR C 53 LYS C 56 5 4 HELIX 31 AD4 PHE C 60 SER C 70 1 11 HELIX 32 AD5 ASN C 82 GLY C 92 1 11 HELIX 33 AD6 ASN C 95 SER C 99 5 5 HELIX 34 AD7 THR C 103 CYS C 109 1 7 HELIX 35 AD8 GLN C 111 ASN C 115 5 5 HELIX 36 AD9 SER C 122 PHE C 134 1 13 HELIX 37 AE1 GLN C 135 LEU C 139 5 5 HELIX 38 AE2 ALA C 146 TYR C 151 1 6 HELIX 39 AE3 LYS D 12 ARG D 18 1 7 HELIX 40 AE4 LEU D 20 GLY D 32 1 13 HELIX 41 AE5 SER D 44 TYR D 52 1 9 HELIX 42 AE6 THR D 53 LYS D 56 5 4 HELIX 43 AE7 PHE D 60 SER D 70 1 11 HELIX 44 AE8 ASN D 82 GLY D 92 1 11 HELIX 45 AE9 ASN D 95 SER D 99 5 5 HELIX 46 AF1 THR D 103 CYS D 109 1 7 HELIX 47 AF2 GLN D 111 ASN D 115 5 5 HELIX 48 AF3 SER D 122 PHE D 134 1 13 HELIX 49 AF4 GLN D 135 LEU D 139 5 5 HELIX 50 AF5 LYS E 12 ARG E 18 1 7 HELIX 51 AF6 LEU E 20 GLY E 32 1 13 HELIX 52 AF7 LYS E 66 GLY E 71 1 6 HELIX 53 AF8 ASN E 82 GLY E 92 1 11 HELIX 54 AF9 THR E 103 CYS E 109 1 7 HELIX 55 AG1 SER E 122 PHE E 134 1 13 HELIX 56 AG2 GLN E 135 LEU E 139 5 5 HELIX 57 AG3 ALA E 146 TYR E 151 1 6 HELIX 58 AG4 MET F 1 SER F 4 5 4 HELIX 59 AG5 LYS F 12 ARG F 18 1 7 HELIX 60 AG6 LEU F 20 GLY F 32 1 13 HELIX 61 AG7 SER F 44 TYR F 52 1 9 HELIX 62 AG8 THR F 53 LYS F 56 5 4 HELIX 63 AG9 PHE F 60 SER F 70 1 11 HELIX 64 AH1 ASN F 82 GLY F 92 1 11 HELIX 65 AH2 ASN F 95 SER F 99 5 5 HELIX 66 AH3 THR F 103 CYS F 109 1 7 HELIX 67 AH4 GLN F 111 ASN F 115 5 5 HELIX 68 AH5 SER F 122 PHE F 134 1 13 HELIX 69 AH6 GLN F 135 LEU F 139 5 5 HELIX 70 AH7 ALA F 146 TYR F 151 1 6 SHEET 1 AA1 4 ARG A 34 LEU A 41 0 SHEET 2 AA1 4 VAL A 73 GLU A 79 -1 O VAL A 73 N LEU A 41 SHEET 3 AA1 4 ARG A 6 ILE A 11 -1 N ILE A 9 O MET A 76 SHEET 4 AA1 4 ILE A 117 GLY A 119 -1 O HIS A 118 N ALA A 10 SHEET 1 AA2 4 ARG B 34 LEU B 41 0 SHEET 2 AA2 4 VAL B 73 GLU B 79 -1 O VAL B 77 N VAL B 36 SHEET 3 AA2 4 ARG B 6 ILE B 11 -1 N ILE B 11 O VAL B 74 SHEET 4 AA2 4 ILE B 117 GLY B 119 -1 O HIS B 118 N ALA B 10 SHEET 1 AA3 4 ARG C 34 LEU C 41 0 SHEET 2 AA3 4 VAL C 73 GLU C 79 -1 O VAL C 73 N LEU C 41 SHEET 3 AA3 4 ARG C 6 ILE C 11 -1 N ILE C 11 O VAL C 74 SHEET 4 AA3 4 ILE C 117 GLY C 119 -1 O HIS C 118 N ALA C 10 SHEET 1 AA4 4 ARG D 34 LEU D 41 0 SHEET 2 AA4 4 VAL D 73 GLU D 79 -1 O VAL D 73 N LEU D 41 SHEET 3 AA4 4 ARG D 6 ILE D 11 -1 N ILE D 11 O VAL D 74 SHEET 4 AA4 4 ILE D 117 GLY D 119 -1 O HIS D 118 N ALA D 10 SHEET 1 AA5 4 ARG E 34 LEU E 41 0 SHEET 2 AA5 4 VAL E 73 GLU E 79 -1 O VAL E 77 N VAL E 36 SHEET 3 AA5 4 ARG E 6 ILE E 11 -1 N ILE E 11 O VAL E 74 SHEET 4 AA5 4 ILE E 117 GLY E 119 -1 O HIS E 118 N ALA E 10 SHEET 1 AA6 4 ARG F 34 LEU F 41 0 SHEET 2 AA6 4 VAL F 73 GLU F 79 -1 O VAL F 73 N LEU F 41 SHEET 3 AA6 4 ARG F 6 ILE F 11 -1 N ILE F 9 O MET F 76 SHEET 4 AA6 4 ILE F 117 GLY F 119 -1 O HIS F 118 N ALA F 10 SSBOND 1 CYS B 145 CYS D 145 1555 1555 2.04 SSBOND 2 CYS C 145 CYS E 145 1555 1555 2.03 CRYST1 51.656 70.193 113.167 90.00 90.96 90.00 P 1 21 1 12 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 0.019359 0.000000 0.000324 0.00000 SCALE2 0.000000 0.014246 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008838 0.00000