HEADER PROTEIN BINDING 12-MAR-25 9M8T TITLE CRYSTAL STRUCTURE OF THE RIBOKINASE RBK1 IN COMPLEX WITH ADP FROM TITLE 2 SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOKINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RK; COMPND 5 EC: 2.7.1.15; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_TAXID: 559292; SOURCE 4 GENE: RBK1, YCR036W, YCR36W, YCR523; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBOKINASE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR X.Y.YANG,X.H.LIU REVDAT 1 04-MAR-26 9M8T 0 JRNL AUTH S.ZHEN,Z.ZHANG,Y.FAN,Y.LI,C.LIU,F.GUO,Y.ZHU,Y.WANG,J.ZHANG, JRNL AUTH 2 J.XIE,H.ZHOU,X.YANG,X.LIU JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO THE MOLECULAR JRNL TITL 2 MECHANISM OF RIBOKINASE RBK1 FROM SACCHAROMYCES CEREVISIAE. JRNL REF INT.J.BIOL.MACROMOL. V. 331 48382 2025 JRNL REFN ISSN 0141-8130 JRNL PMID 41110570 JRNL DOI 10.1016/J.IJBIOMAC.2025.148382 REMARK 2 REMARK 2 RESOLUTION. 2.66 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) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 24282 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 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 31.8800 - 5.5300 0.99 2726 129 0.1725 0.2386 REMARK 3 2 5.5200 - 4.3900 1.00 2633 156 0.1713 0.1941 REMARK 3 3 4.3900 - 3.8300 0.98 2567 133 0.2028 0.3285 REMARK 3 4 3.8300 - 3.4800 0.93 2434 127 0.2592 0.2851 REMARK 3 5 3.4800 - 3.2400 0.98 2527 143 0.2619 0.3665 REMARK 3 6 3.2400 - 3.0400 1.00 2568 142 0.2670 0.3356 REMARK 3 7 3.0400 - 2.8900 0.99 2566 133 0.3034 0.3598 REMARK 3 8 2.8900 - 2.7700 0.99 2579 115 0.2946 0.3627 REMARK 3 9 2.7700 - 2.6600 0.96 2465 139 0.3801 0.4260 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 5247 REMARK 3 ANGLE : 1.212 7120 REMARK 3 CHIRALITY : 0.067 814 REMARK 3 PLANARITY : 0.006 916 REMARK 3 DIHEDRAL : 18.914 1914 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 22.0256 30.7205 82.7041 REMARK 3 T TENSOR REMARK 3 T11: 0.4331 T22: 0.5246 REMARK 3 T33: 0.5093 T12: 0.0212 REMARK 3 T13: 0.0193 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: -0.1108 L22: 0.7751 REMARK 3 L33: 0.6640 L12: 0.0658 REMARK 3 L13: 0.0309 L23: -0.3915 REMARK 3 S TENSOR REMARK 3 S11: -0.0094 S12: 0.0466 S13: 0.0506 REMARK 3 S21: 0.0174 S22: 0.0555 S23: 0.0420 REMARK 3 S31: -0.0434 S32: -0.0622 S33: -0.0000 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 9M8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-23 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24435 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.660 REMARK 200 RESOLUTION RANGE LOW (A) : 40.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% TACSIMATE PH 8.0, 20% PEG 3350, REMARK 280 0.02M CALCIUM CHLORIDE DIHYDRATE, VAPOR DIFFUSION, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.82000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.57500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 84.14500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.82000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.57500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 84.14500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.82000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.57500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.14500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.82000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.57500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 84.14500 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: 5390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 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 19 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 106 CB CG CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 VAL A 210 CG1 CG2 REMARK 470 GLU A 211 OE2 REMARK 470 ARG A 214 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 ARG A 239 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 ARG A 242 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 331 CG CD CE NZ REMARK 470 GLU B 92 CG CD OE1 OE2 REMARK 470 LYS B 106 CG CD CE NZ REMARK 470 VAL B 210 CG1 CG2 REMARK 470 GLU B 211 OE2 REMARK 470 ARG B 214 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 234 CG CD OE1 OE2 REMARK 470 LYS B 235 CG CD CE NZ REMARK 470 LEU B 236 CG CD1 CD2 REMARK 470 ARG B 239 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 241 CG CD CE NZ REMARK 470 ARG B 242 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 259 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 331 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 175 N - CA - C ANGL. DEV. = -18.5 DEGREES REMARK 500 PRO B 175 N - CA - C ANGL. DEV. = -17.2 DEGREES 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 VAL A 65 -169.44 -110.84 REMARK 500 THR A 90 82.21 -150.13 REMARK 500 LYS A 106 -33.84 75.47 REMARK 500 ALA A 107 -152.15 -76.90 REMARK 500 ARG A 112 124.79 -176.75 REMARK 500 PHE A 134 77.12 -113.59 REMARK 500 LYS A 138 108.29 -56.46 REMARK 500 GLN A 147 -148.87 -123.42 REMARK 500 ARG A 164 53.02 -141.15 REMARK 500 SER A 174 -70.05 -76.59 REMARK 500 PRO A 175 97.57 -67.15 REMARK 500 PHE A 205 -140.94 -113.80 REMARK 500 ASP A 206 -158.19 -139.95 REMARK 500 VAL A 210 -51.41 -126.11 REMARK 500 ASP A 220 79.59 -163.42 REMARK 500 LYS A 235 21.45 -143.06 REMARK 500 LEU A 236 -35.76 -158.25 REMARK 500 GLU A 263 155.56 71.29 REMARK 500 ASN A 272 69.45 37.15 REMARK 500 ALA A 319 -105.23 -108.17 REMARK 500 ALA B 29 -165.64 -78.35 REMARK 500 ASN B 52 106.69 -56.46 REMARK 500 SER B 55 13.66 -154.38 REMARK 500 ARG B 56 -69.56 65.19 REMARK 500 LYS B 106 -147.82 -89.61 REMARK 500 ALA B 107 -72.79 -61.19 REMARK 500 GLN B 110 59.99 31.98 REMARK 500 GLN B 147 -145.70 -121.73 REMARK 500 HIS B 148 30.62 -140.93 REMARK 500 PHE B 205 -140.92 -113.74 REMARK 500 ASP B 206 -158.21 -139.98 REMARK 500 VAL B 210 -51.40 -126.09 REMARK 500 ASP B 220 79.62 -163.41 REMARK 500 LYS B 235 -96.72 -101.33 REMARK 500 SER B 258 -153.51 -134.99 REMARK 500 LEU B 267 114.33 -161.59 REMARK 500 VAL B 276 -54.24 -120.67 REMARK 500 ALA B 319 -116.57 -107.62 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 60 0.26 SIDE CHAIN 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 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 279 O REMARK 620 2 THR A 313 O 115.6 REMARK 620 3 GLY A 318 O 83.3 142.7 REMARK 620 4 SER A 322 OG 108.6 67.9 75.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 401 O2B REMARK 620 2 ADP A 401 O2A 78.1 REMARK 620 3 HOH A 511 O 64.8 134.9 REMARK 620 4 HOH A 536 O 99.9 74.7 86.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 318 O REMARK 620 2 SER B 322 OG 96.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP B 401 O2B REMARK 620 2 ADP B 401 O2A 73.5 REMARK 620 3 HOH B 508 O 136.3 63.7 REMARK 620 4 HOH B 521 O 148.9 127.2 71.6 REMARK 620 N 1 2 3 DBREF 9M8T A 1 333 UNP P25332 RBSK_YEAST 1 333 DBREF 9M8T B 1 333 UNP P25332 RBSK_YEAST 1 333 SEQRES 1 A 333 MET GLY ILE THR VAL ILE GLY SER LEU ASN TYR ASP LEU SEQRES 2 A 333 ASP THR PHE THR ASP ARG LEU PRO ASN ALA GLY GLU THR SEQRES 3 A 333 PHE ARG ALA ASN HIS PHE GLU THR HIS ALA GLY GLY LYS SEQRES 4 A 333 GLY LEU ASN GLN ALA ALA ALA ILE GLY LYS LEU LYS ASN SEQRES 5 A 333 PRO SER SER ARG TYR SER VAL ARG MET ILE GLY ASN VAL SEQRES 6 A 333 GLY ASN ASP THR PHE GLY LYS GLN LEU LYS ASP THR LEU SEQRES 7 A 333 SER ASP CYS GLY VAL ASP ILE THR HIS VAL GLY THR TYR SEQRES 8 A 333 GLU GLY ILE ASN THR GLY THR ALA THR ILE LEU ILE GLU SEQRES 9 A 333 GLU LYS ALA GLY GLY GLN ASN ARG ILE LEU ILE VAL GLU SEQRES 10 A 333 GLY ALA ASN SER LYS THR ILE TYR ASP PRO LYS GLN LEU SEQRES 11 A 333 CYS GLU ILE PHE PRO GLU GLY LYS GLU GLU GLU GLU TYR SEQRES 12 A 333 VAL VAL PHE GLN HIS GLU ILE PRO ASP PRO LEU SER ILE SEQRES 13 A 333 ILE LYS TRP ILE HIS ALA ASN ARG PRO ASN PHE GLN ILE SEQRES 14 A 333 VAL TYR ASN PRO SER PRO PHE LYS ALA MET PRO LYS LYS SEQRES 15 A 333 ASP TRP GLU LEU VAL ASP LEU LEU VAL VAL ASN GLU ILE SEQRES 16 A 333 GLU GLY LEU GLN ILE VAL GLU SER VAL PHE ASP ASN GLU SEQRES 17 A 333 LEU VAL GLU GLU ILE ARG GLU LYS ILE LYS ASP ASP PHE SEQRES 18 A 333 LEU GLY GLU TYR ARG LYS ILE CYS GLU LEU LEU TYR GLU SEQRES 19 A 333 LYS LEU MET ASN ARG LYS LYS ARG GLY ILE VAL VAL MET SEQRES 20 A 333 THR LEU GLY SER ARG GLY VAL LEU PHE CYS SER HIS GLU SEQRES 21 A 333 SER PRO GLU VAL GLN PHE LEU PRO ALA ILE GLN ASN VAL SEQRES 22 A 333 SER VAL VAL ASP THR THR GLY ALA GLY ASP THR PHE LEU SEQRES 23 A 333 GLY GLY LEU VAL THR GLN LEU TYR GLN GLY GLU THR LEU SEQRES 24 A 333 SER THR ALA ILE LYS PHE SER THR LEU ALA SER SER LEU SEQRES 25 A 333 THR ILE GLN ARG LYS GLY ALA ALA GLU SER MET PRO LEU SEQRES 26 A 333 TYR LYS ASP VAL GLN LYS ASP ALA SEQRES 1 B 333 MET GLY ILE THR VAL ILE GLY SER LEU ASN TYR ASP LEU SEQRES 2 B 333 ASP THR PHE THR ASP ARG LEU PRO ASN ALA GLY GLU THR SEQRES 3 B 333 PHE ARG ALA ASN HIS PHE GLU THR HIS ALA GLY GLY LYS SEQRES 4 B 333 GLY LEU ASN GLN ALA ALA ALA ILE GLY LYS LEU LYS ASN SEQRES 5 B 333 PRO SER SER ARG TYR SER VAL ARG MET ILE GLY ASN VAL SEQRES 6 B 333 GLY ASN ASP THR PHE GLY LYS GLN LEU LYS ASP THR LEU SEQRES 7 B 333 SER ASP CYS GLY VAL ASP ILE THR HIS VAL GLY THR TYR SEQRES 8 B 333 GLU GLY ILE ASN THR GLY THR ALA THR ILE LEU ILE GLU SEQRES 9 B 333 GLU LYS ALA GLY GLY GLN ASN ARG ILE LEU ILE VAL GLU SEQRES 10 B 333 GLY ALA ASN SER LYS THR ILE TYR ASP PRO LYS GLN LEU SEQRES 11 B 333 CYS GLU ILE PHE PRO GLU GLY LYS GLU GLU GLU GLU TYR SEQRES 12 B 333 VAL VAL PHE GLN HIS GLU ILE PRO ASP PRO LEU SER ILE SEQRES 13 B 333 ILE LYS TRP ILE HIS ALA ASN ARG PRO ASN PHE GLN ILE SEQRES 14 B 333 VAL TYR ASN PRO SER PRO PHE LYS ALA MET PRO LYS LYS SEQRES 15 B 333 ASP TRP GLU LEU VAL ASP LEU LEU VAL VAL ASN GLU ILE SEQRES 16 B 333 GLU GLY LEU GLN ILE VAL GLU SER VAL PHE ASP ASN GLU SEQRES 17 B 333 LEU VAL GLU GLU ILE ARG GLU LYS ILE LYS ASP ASP PHE SEQRES 18 B 333 LEU GLY GLU TYR ARG LYS ILE CYS GLU LEU LEU TYR GLU SEQRES 19 B 333 LYS LEU MET ASN ARG LYS LYS ARG GLY ILE VAL VAL MET SEQRES 20 B 333 THR LEU GLY SER ARG GLY VAL LEU PHE CYS SER HIS GLU SEQRES 21 B 333 SER PRO GLU VAL GLN PHE LEU PRO ALA ILE GLN ASN VAL SEQRES 22 B 333 SER VAL VAL ASP THR THR GLY ALA GLY ASP THR PHE LEU SEQRES 23 B 333 GLY GLY LEU VAL THR GLN LEU TYR GLN GLY GLU THR LEU SEQRES 24 B 333 SER THR ALA ILE LYS PHE SER THR LEU ALA SER SER LEU SEQRES 25 B 333 THR ILE GLN ARG LYS GLY ALA ALA GLU SER MET PRO LEU SEQRES 26 B 333 TYR LYS ASP VAL GLN LYS ASP ALA HET ADP A 401 27 HET MG A 402 1 HET PO4 A 403 5 HET NA A 404 1 HET ADP B 401 27 HET MG B 402 1 HET PO4 B 403 5 HET NA B 404 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 MG 2(MG 2+) FORMUL 5 PO4 2(O4 P 3-) FORMUL 6 NA 2(NA 1+) FORMUL 11 HOH *109(H2 O) HELIX 1 AA1 GLY A 38 LYS A 51 1 14 HELIX 2 AA2 ASP A 68 CYS A 81 1 14 HELIX 3 AA3 GLU A 117 THR A 123 5 7 HELIX 4 AA4 ASP A 126 PHE A 134 1 9 HELIX 5 AA5 ASP A 152 ARG A 164 1 13 HELIX 6 AA6 PRO A 180 GLU A 185 1 6 HELIX 7 AA7 GLU A 194 PHE A 205 1 12 HELIX 8 AA8 ASN A 207 ASP A 220 1 14 HELIX 9 AA9 ASP A 220 LYS A 235 1 16 HELIX 10 AB1 GLY A 250 ARG A 252 5 3 HELIX 11 AB2 GLY A 280 GLN A 295 1 16 HELIX 12 AB3 THR A 298 GLN A 315 1 18 HELIX 13 AB4 ALA A 319 MET A 323 5 5 HELIX 14 AB5 LEU A 325 ALA A 333 1 9 HELIX 15 AB6 GLY B 38 LYS B 51 1 14 HELIX 16 AB7 ASP B 68 GLY B 82 1 15 HELIX 17 AB8 GLU B 117 THR B 123 5 7 HELIX 18 AB9 ASP B 126 PHE B 134 1 9 HELIX 19 AC1 ASP B 152 ARG B 164 1 13 HELIX 20 AC2 PRO B 180 GLU B 185 1 6 HELIX 21 AC3 GLU B 194 PHE B 205 1 12 HELIX 22 AC4 ASN B 207 ASP B 220 1 14 HELIX 23 AC5 ASP B 220 LYS B 235 1 16 HELIX 24 AC6 GLY B 250 ARG B 252 5 3 HELIX 25 AC7 GLY B 280 GLN B 295 1 16 HELIX 26 AC8 THR B 298 ARG B 316 1 19 HELIX 27 AC9 LEU B 325 LYS B 331 1 7 SHEET 1 AA1 9 VAL A 88 TYR A 91 0 SHEET 2 AA1 9 SER A 58 GLY A 66 1 N VAL A 65 O GLY A 89 SHEET 3 AA1 9 GLY A 2 ILE A 6 1 N VAL A 5 O ILE A 62 SHEET 4 AA1 9 TYR A 143 PHE A 146 1 O VAL A 145 N THR A 4 SHEET 5 AA1 9 GLN A 168 TYR A 171 1 O VAL A 170 N VAL A 144 SHEET 6 AA1 9 LEU A 189 ASN A 193 1 O LEU A 189 N TYR A 171 SHEET 7 AA1 9 ILE A 244 THR A 248 1 O VAL A 246 N LEU A 190 SHEET 8 AA1 9 VAL A 254 SER A 258 -1 O LEU A 255 N MET A 247 SHEET 9 AA1 9 GLN A 265 LEU A 267 -1 O GLN A 265 N PHE A 256 SHEET 1 AA2 5 HIS A 31 GLY A 37 0 SHEET 2 AA2 5 ASN A 10 THR A 17 -1 N ASP A 14 O GLU A 33 SHEET 3 AA2 5 GLY A 97 GLU A 104 1 O ALA A 99 N LEU A 13 SHEET 4 AA2 5 ASN A 111 VAL A 116 -1 O ARG A 112 N LEU A 102 SHEET 5 AA2 5 THR B 26 ARG B 28 1 O PHE B 27 N ILE A 115 SHEET 1 AA3 5 THR A 26 ARG A 28 0 SHEET 2 AA3 5 ARG B 112 VAL B 116 1 O ILE B 113 N PHE A 27 SHEET 3 AA3 5 GLY B 97 GLU B 104 -1 N THR B 100 O LEU B 114 SHEET 4 AA3 5 ASN B 10 THR B 17 1 N LEU B 13 O ALA B 99 SHEET 5 AA3 5 HIS B 31 GLY B 37 -1 O GLU B 33 N ASP B 14 SHEET 1 AA4 9 ASP B 84 TYR B 91 0 SHEET 2 AA4 9 VAL B 59 GLY B 66 1 N VAL B 59 O ASP B 84 SHEET 3 AA4 9 ILE B 3 ILE B 6 1 N VAL B 5 O ILE B 62 SHEET 4 AA4 9 TYR B 143 PHE B 146 1 O VAL B 145 N ILE B 6 SHEET 5 AA4 9 GLN B 168 TYR B 171 1 O VAL B 170 N PHE B 146 SHEET 6 AA4 9 LEU B 189 ASN B 193 1 O LEU B 189 N TYR B 171 SHEET 7 AA4 9 ILE B 244 THR B 248 1 O VAL B 246 N LEU B 190 SHEET 8 AA4 9 VAL B 254 CYS B 257 -1 O LEU B 255 N MET B 247 SHEET 9 AA4 9 GLN B 265 LEU B 267 -1 O GLN B 265 N PHE B 256 LINK O THR A 279 NA NA A 404 1555 1555 3.05 LINK O THR A 313 NA NA A 404 1555 1555 3.13 LINK O GLY A 318 NA NA A 404 1555 1555 2.38 LINK OG SER A 322 NA NA A 404 1555 1555 3.06 LINK O2B ADP A 401 MG MG A 402 1555 1555 2.42 LINK O2A ADP A 401 MG MG A 402 1555 1555 2.53 LINK MG MG A 402 O HOH A 511 1555 1555 2.26 LINK MG MG A 402 O HOH A 536 1555 1555 2.12 LINK O GLY B 318 NA NA B 404 1555 1555 2.24 LINK OG SER B 322 NA NA B 404 1555 1555 2.50 LINK O2B ADP B 401 MG MG B 402 1555 1555 2.52 LINK O2A ADP B 401 MG MG B 402 1555 1555 2.49 LINK MG MG B 402 O HOH B 508 1555 1555 2.20 LINK MG MG B 402 O HOH B 521 1555 1555 2.18 CRYST1 81.640 123.150 168.290 90.00 90.00 90.00 I 2 2 2 16 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 0.012249 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005942 0.00000 CONECT 2146 5125 CONECT 2388 5125 CONECT 2432 5125 CONECT 2457 5125 CONECT 4978 5159 CONECT 5003 5159 CONECT 5092 5093 5094 5095 5099 CONECT 5093 5092 CONECT 5094 5092 5119 CONECT 5095 5092 CONECT 5096 5097 5098 5099 5100 CONECT 5097 5096 CONECT 5098 5096 5119 CONECT 5099 5092 5096 CONECT 5100 5096 5101 CONECT 5101 5100 5102 CONECT 5102 5101 5103 5104 CONECT 5103 5102 5108 CONECT 5104 5102 5105 5106 CONECT 5105 5104 CONECT 5106 5104 5107 5108 CONECT 5107 5106 CONECT 5108 5103 5106 5109 CONECT 5109 5108 5110 5118 CONECT 5110 5109 5111 CONECT 5111 5110 5112 CONECT 5112 5111 5113 5118 CONECT 5113 5112 5114 5115 CONECT 5114 5113 CONECT 5115 5113 5116 CONECT 5116 5115 5117 CONECT 5117 5116 5118 CONECT 5118 5109 5112 5117 CONECT 5119 5094 5098 5170 5195 CONECT 5120 5121 5122 5123 5124 CONECT 5121 5120 CONECT 5122 5120 CONECT 5123 5120 CONECT 5124 5120 CONECT 5125 2146 2388 2432 2457 CONECT 5126 5127 5128 5129 5133 CONECT 5127 5126 CONECT 5128 5126 5153 CONECT 5129 5126 CONECT 5130 5131 5132 5133 5134 CONECT 5131 5130 CONECT 5132 5130 5153 CONECT 5133 5126 5130 CONECT 5134 5130 5135 CONECT 5135 5134 5136 CONECT 5136 5135 5137 5138 CONECT 5137 5136 5142 CONECT 5138 5136 5139 5140 CONECT 5139 5138 CONECT 5140 5138 5141 5142 CONECT 5141 5140 CONECT 5142 5137 5140 5143 CONECT 5143 5142 5144 5152 CONECT 5144 5143 5145 CONECT 5145 5144 5146 CONECT 5146 5145 5147 5152 CONECT 5147 5146 5148 5149 CONECT 5148 5147 CONECT 5149 5147 5150 CONECT 5150 5149 5151 CONECT 5151 5150 5152 CONECT 5152 5143 5146 5151 CONECT 5153 5128 5132 5222 5235 CONECT 5154 5155 5156 5157 5158 CONECT 5155 5154 CONECT 5156 5154 CONECT 5157 5154 CONECT 5158 5154 CONECT 5159 4978 5003 CONECT 5170 5119 CONECT 5195 5119 CONECT 5222 5153 CONECT 5235 5153 MASTER 392 0 8 27 28 0 0 6 5266 2 78 52 END