HEADER TRANSFERASE 10-SEP-13 4C58 TITLE STRUCTURE OF GAK KINASE IN COMPLEX WITH NANOBODY (NBGAK_4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-G-ASSOCIATED KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 27-351; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NANOBODY; COMPND 9 CHAIN: B; COMPND 10 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: GAK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: R3; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 14 ORGANISM_COMMON: LLAMA; SOURCE 15 ORGANISM_TAXID: 9844; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, KINASE, CONFORMATIONAL PLASTICITY, ACTIVATION EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAIKUAD,T.KEATES,C.K.ALLERSTON,O.GILEADI,F.VON DELFT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,S.KNAPP,S.MULLER-KNAPP REVDAT 5 13-NOV-24 4C58 1 REMARK REVDAT 4 20-DEC-23 4C58 1 REMARK REVDAT 3 06-FEB-19 4C58 1 COMPND SOURCE JRNL REMARK REVDAT 3 2 1 DBREF SEQADV REVDAT 2 09-APR-14 4C58 1 JRNL REVDAT 1 09-OCT-13 4C58 0 JRNL AUTH A.CHAIKUAD,T.KEATES,C.VINCKE,M.KAUFHOLZ,M.ZENN,B.ZIMMERMANN, JRNL AUTH 2 C.GUTIERREZ,R.G.ZHANG,C.HATZOS-SKINTGES,A.JOACHIMIAK, JRNL AUTH 3 S.MUYLDERMANS,F.W.HERBERG,S.KNAPP,S.MULLER JRNL TITL STRUCTURE OF CYCLIN G-ASSOCIATED KINASE (GAK) TRAPPED IN JRNL TITL 2 DIFFERENT CONFORMATIONS USING NANOBODIES. JRNL REF BIOCHEM. J. V. 459 59 2014 JRNL REFN ESSN 1470-8728 JRNL PMID 24438162 JRNL DOI 10.1042/BJ20131399 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 21576 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1170 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1525 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2985 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.99000 REMARK 3 B22 (A**2) : 2.15000 REMARK 3 B33 (A**2) : -1.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.244 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.207 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.053 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3120 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2123 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4229 ; 1.596 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5170 ; 0.921 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 6.550 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;37.145 ;23.913 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 531 ;15.268 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.143 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 475 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3493 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 637 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 27 A 89 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3880 20.6090 -52.3300 REMARK 3 T TENSOR REMARK 3 T11: 0.3765 T22: 0.6761 REMARK 3 T33: 0.1110 T12: 0.1177 REMARK 3 T13: 0.0560 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 10.5536 L22: 0.9876 REMARK 3 L33: 4.3863 L12: -1.5509 REMARK 3 L13: -1.5001 L23: 0.6036 REMARK 3 S TENSOR REMARK 3 S11: 0.2040 S12: 1.6098 S13: -0.3602 REMARK 3 S21: -0.4354 S22: -0.2320 S23: -0.1109 REMARK 3 S31: 0.3727 S32: 0.4711 S33: 0.0280 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 90 A 333 REMARK 3 ORIGIN FOR THE GROUP (A): 32.3790 19.5090 -29.4240 REMARK 3 T TENSOR REMARK 3 T11: 0.0878 T22: 0.1032 REMARK 3 T33: 0.0057 T12: -0.0061 REMARK 3 T13: 0.0061 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 2.5798 L22: 1.2211 REMARK 3 L33: 3.1942 L12: -0.0199 REMARK 3 L13: 0.8154 L23: -0.4372 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: 0.4803 S13: -0.0380 REMARK 3 S21: -0.1220 S22: -0.0277 S23: -0.0780 REMARK 3 S31: 0.1583 S32: 0.1746 S33: 0.0288 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 128 REMARK 3 ORIGIN FOR THE GROUP (A): 26.7180 31.6100 -1.1160 REMARK 3 T TENSOR REMARK 3 T11: 0.1523 T22: 0.0154 REMARK 3 T33: 0.0504 T12: -0.0354 REMARK 3 T13: 0.0288 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 2.1553 L22: 2.6037 REMARK 3 L33: 3.8626 L12: 0.5304 REMARK 3 L13: 0.4243 L23: 1.5296 REMARK 3 S TENSOR REMARK 3 S11: 0.1497 S12: -0.0577 S13: 0.1999 REMARK 3 S21: 0.1028 S22: -0.0821 S23: 0.2307 REMARK 3 S31: -0.3193 S32: 0.1362 S33: -0.0676 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4C58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1290058293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-12 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0121 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22748 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 45.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: PDB ENTRIES 3LL6 AND 1OP9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3350, 0.13 M MAGNESIUM REMARK 280 FORMATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 78.43300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.43300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.71500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.3 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 -1.000000 0.000000 0.000000 24.09316 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -72.09050 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 SER A 12 REMARK 465 MET A 13 REMARK 465 PRO A 14 REMARK 465 GLY A 15 REMARK 465 SER A 16 REMARK 465 LEU A 17 REMARK 465 GLY A 18 REMARK 465 GLY A 19 REMARK 465 ALA A 20 REMARK 465 SER A 21 REMARK 465 GLY A 22 REMARK 465 ARG A 23 REMARK 465 ASP A 24 REMARK 465 GLN A 25 REMARK 465 SER A 26 REMARK 465 TYR A 204 REMARK 465 SER A 205 REMARK 465 TRP A 206 REMARK 465 SER A 207 REMARK 465 ALA A 208 REMARK 465 GLN A 209 REMARK 465 ARG A 210 REMARK 465 ARG A 211 REMARK 465 ALA A 212 REMARK 465 LEU A 213 REMARK 465 VAL A 214 REMARK 465 GLU A 215 REMARK 465 GLU A 216 REMARK 465 GLU A 217 REMARK 465 ILE A 218 REMARK 465 THR A 219 REMARK 465 ARG A 220 REMARK 465 ASN A 221 REMARK 465 THR A 222 REMARK 465 THR A 223 REMARK 465 PRO A 224 REMARK 465 MET A 225 REMARK 465 TYR A 226 REMARK 465 ARG A 227 REMARK 465 THR A 228 REMARK 465 PRO A 229 REMARK 465 GLU A 230 REMARK 465 ILE A 231 REMARK 465 ILE A 232 REMARK 465 ASP A 233 REMARK 465 ASP A 265 REMARK 465 GLY A 266 REMARK 465 ALA A 267 REMARK 465 LYS A 268 REMARK 465 LEU A 269 REMARK 465 ARG A 270 REMARK 465 ILE A 271 REMARK 465 VAL A 272 REMARK 465 ASN A 273 REMARK 465 GLY A 274 REMARK 465 GLN A 334 REMARK 465 ASN A 335 REMARK 465 GLY A 336 REMARK 465 GLY A 337 REMARK 465 TYR A 338 REMARK 465 GLY A 339 REMARK 465 SER A 340 REMARK 465 ALA A 341 REMARK 465 THR A 342 REMARK 465 LEU A 343 REMARK 465 SER A 344 REMARK 465 ARG A 345 REMARK 465 GLY A 346 REMARK 465 PRO A 347 REMARK 465 PRO A 348 REMARK 465 PRO A 349 REMARK 465 PRO A 350 REMARK 465 VAL A 351 REMARK 465 ALA B 129 REMARK 465 ALA B 130 REMARK 465 ALA B 131 REMARK 465 TYR B 132 REMARK 465 PRO B 133 REMARK 465 TYR B 134 REMARK 465 ASP B 135 REMARK 465 VAL B 136 REMARK 465 PRO B 137 REMARK 465 ASP B 138 REMARK 465 TYR B 139 REMARK 465 GLY B 140 REMARK 465 SER B 141 REMARK 465 HIS B 142 REMARK 465 HIS B 143 REMARK 465 HIS B 144 REMARK 465 HIS B 145 REMARK 465 HIS B 146 REMARK 465 HIS B 147 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 ASP A 27 CG OD1 OD2 REMARK 470 ARG A 41 CD NE CZ NH1 NH2 REMARK 470 ARG A 43 NE CZ NH1 NH2 REMARK 470 PHE A 51 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 107 CG1 CG2 CD1 REMARK 470 ASP A 113 CG OD1 OD2 REMARK 470 ASP A 203 CG OD1 OD2 REMARK 470 LEU A 234 CG CD1 CD2 REMARK 470 TYR A 235 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 264 CG CD OE1 OE2 REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 SER B 128 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 163 CG HIS A 163 CD2 0.056 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 293 NE - CZ - NH2 ANGL. DEV. = -3.9 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 GLU A 48 -127.67 -135.84 REMARK 500 ASP A 113 36.96 -89.85 REMARK 500 ARG A 172 -1.84 69.14 REMARK 500 THR A 197 -163.92 -168.19 REMARK 500 SER A 236 119.47 -168.13 REMARK 500 SER B 93 48.22 38.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 824 A 1336 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C57 RELATED DB: PDB REMARK 900 STRUCTURE OF GAK KINASE IN COMPLEX WITH A NANOBODY REMARK 900 RELATED ID: 4C59 RELATED DB: PDB REMARK 900 STRUCTURE OF GAK KINASE IN COMPLEX WITH NANOBODY ( NBGAK_4) REMARK 999 REMARK 999 SEQUENCE REMARK 999 SYNTHETIC, NON-BIOLOGICAL SEQUENCE DBREF 4C58 A 14 351 UNP O14976 GAK_HUMAN 14 351 DBREF 4C58 B 1 147 PDB 4C58 4C58 1 147 SEQADV 4C58 SER A 12 UNP O14976 EXPRESSION TAG SEQADV 4C58 MET A 13 UNP O14976 EXPRESSION TAG SEQRES 1 A 340 SER MET PRO GLY SER LEU GLY GLY ALA SER GLY ARG ASP SEQRES 2 A 340 GLN SER ASP PHE VAL GLY GLN THR VAL GLU LEU GLY GLU SEQRES 3 A 340 LEU ARG LEU ARG VAL ARG ARG VAL LEU ALA GLU GLY GLY SEQRES 4 A 340 PHE ALA PHE VAL TYR GLU ALA GLN ASP VAL GLY SER GLY SEQRES 5 A 340 ARG GLU TYR ALA LEU LYS ARG LEU LEU SER ASN GLU GLU SEQRES 6 A 340 GLU LYS ASN ARG ALA ILE ILE GLN GLU VAL CYS PHE MET SEQRES 7 A 340 LYS LYS LEU SER GLY HIS PRO ASN ILE VAL GLN PHE CYS SEQRES 8 A 340 SER ALA ALA SER ILE GLY LYS GLU GLU SER ASP THR GLY SEQRES 9 A 340 GLN ALA GLU PHE LEU LEU LEU THR GLU LEU CYS LYS GLY SEQRES 10 A 340 GLN LEU VAL GLU PHE LEU LYS LYS MET GLU SER ARG GLY SEQRES 11 A 340 PRO LEU SER CYS ASP THR VAL LEU LYS ILE PHE TYR GLN SEQRES 12 A 340 THR CYS ARG ALA VAL GLN HIS MET HIS ARG GLN LYS PRO SEQRES 13 A 340 PRO ILE ILE HIS ARG ASP LEU LYS VAL GLU ASN LEU LEU SEQRES 14 A 340 LEU SER ASN GLN GLY THR ILE LYS LEU CYS ASP PHE GLY SEQRES 15 A 340 SER ALA THR THR ILE SER HIS TYR PRO ASP TYR SER TRP SEQRES 16 A 340 SER ALA GLN ARG ARG ALA LEU VAL GLU GLU GLU ILE THR SEQRES 17 A 340 ARG ASN THR THR PRO MET TYR ARG THR PRO GLU ILE ILE SEQRES 18 A 340 ASP LEU TYR SER ASN PHE PRO ILE GLY GLU LYS GLN ASP SEQRES 19 A 340 ILE TRP ALA LEU GLY CYS ILE LEU TYR LEU LEU CYS PHE SEQRES 20 A 340 ARG GLN HIS PRO PHE GLU ASP GLY ALA LYS LEU ARG ILE SEQRES 21 A 340 VAL ASN GLY LYS TYR SER ILE PRO PRO HIS ASP THR GLN SEQRES 22 A 340 TYR THR VAL PHE HIS SER LEU ILE ARG ALA MET LEU GLN SEQRES 23 A 340 VAL ASN PRO GLU GLU ARG LEU SER ILE ALA GLU VAL VAL SEQRES 24 A 340 HIS GLN LEU GLN GLU ILE ALA ALA ALA ARG ASN VAL ASN SEQRES 25 A 340 PRO LYS SER PRO ILE THR GLU LEU LEU GLU GLN ASN GLY SEQRES 26 A 340 GLY TYR GLY SER ALA THR LEU SER ARG GLY PRO PRO PRO SEQRES 27 A 340 PRO VAL SEQRES 1 B 140 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 B 140 ALA GLY GLY SER LEU ARG LEU SER CYS GLY ALA SER GLU SEQRES 3 B 140 TYR THR SER ARG MET GLY TRP PHE ARG GLN ALA PRO GLY SEQRES 4 B 140 ALA GLU ARG GLU GLY VAL ALA CYS ILE HIS ARG GLN SER SEQRES 5 B 140 ASN LEU SER TYR TYR SER ASP SER VAL ARG GLY ARG PHE SEQRES 6 B 140 THR ILE SER GLN ASP ASN ALA LYS THR THR ALA PHE LEU SEQRES 7 B 140 LEU MET SER SER LEU LYS PRO GLU ASP THR ALA ILE TYR SEQRES 8 B 140 TYR CYS ALA THR THR THR ASP CYS ALA ALA PHE VAL GLU SEQRES 9 B 140 ARG ALA THR ALA ILE THR ALA GLY GLN GLY THR GLN VAL SEQRES 10 B 140 THR VAL SER SER ALA ALA ALA TYR PRO TYR ASP VAL PRO SEQRES 11 B 140 ASP TYR GLY SER HIS HIS HIS HIS HIS HIS HET EDO A1334 4 HET EDO A1335 4 HET 824 A1336 25 HET EDO B1129 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM 824 9-HYDROXY-4-PHENYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)- HETNAM 2 824 DIONE HETSYN EDO ETHYLENE GLYCOL HETSYN 824 9-HYDROXY-4-PHENYL-6H-PYRROLO[3,4-C]CARBAZOLE-1,3-DIONE FORMUL 3 EDO 3(C2 H6 O2) FORMUL 5 824 C20 H12 N2 O3 FORMUL 7 HOH *194(H2 O) HELIX 1 1 GLU A 75 SER A 93 1 19 HELIX 2 2 GLY A 108 SER A 112 5 5 HELIX 3 3 LEU A 130 SER A 139 1 10 HELIX 4 4 SER A 144 ARG A 164 1 21 HELIX 5 5 LYS A 175 ASN A 178 5 4 HELIX 6 6 GLY A 241 ARG A 259 1 19 HELIX 7 7 TYR A 285 VAL A 287 5 3 HELIX 8 8 PHE A 288 LEU A 296 1 9 HELIX 9 9 SER A 305 ARG A 320 1 16 HELIX 10 10 ILE A 328 LEU A 332 5 5 HELIX 11 11 LYS B 95 THR B 99 5 5 HELIX 12 12 ASP B 109 ALA B 113 1 9 SHEET 1 AA 6 THR A 32 LEU A 35 0 SHEET 2 AA 6 LEU A 38 ALA A 47 -1 O LEU A 38 N LEU A 35 SHEET 3 AA 6 ALA A 52 ASP A 59 -1 O VAL A 54 N LEU A 46 SHEET 4 AA 6 GLU A 65 SER A 73 -1 O TYR A 66 N ALA A 57 SHEET 5 AA 6 ALA A 117 THR A 123 -1 O ALA A 117 N SER A 73 SHEET 6 AA 6 PHE A 101 ILE A 107 -1 N CYS A 102 O LEU A 122 SHEET 1 AB 3 GLY A 128 GLN A 129 0 SHEET 2 AB 3 LEU A 180 LEU A 181 -1 N LEU A 181 O GLY A 128 SHEET 3 AB 3 ILE A 187 LYS A 188 -1 O LYS A 188 N LEU A 180 SHEET 1 BA 4 LEU B 4 GLY B 8 0 SHEET 2 BA 4 LEU B 19 ALA B 25 -1 O SER B 22 N SER B 7 SHEET 3 BA 4 THR B 86 MET B 91 -1 O ALA B 87 N CYS B 23 SHEET 4 BA 4 PHE B 76 GLN B 80 -1 O THR B 77 N LEU B 90 SHEET 1 BB 4 GLY B 11 VAL B 13 0 SHEET 2 BB 4 THR B 122 VAL B 126 1 O GLN B 123 N GLY B 11 SHEET 3 BB 4 ALA B 100 THR B 106 -1 O ALA B 100 N VAL B 124 SHEET 4 BB 4 THR B 117 ALA B 118 -1 O THR B 117 N THR B 106 SHEET 1 BC 6 GLY B 11 VAL B 13 0 SHEET 2 BC 6 THR B 122 VAL B 126 1 O GLN B 123 N GLY B 11 SHEET 3 BC 6 ALA B 100 THR B 106 -1 O ALA B 100 N VAL B 124 SHEET 4 BC 6 ARG B 34 GLN B 44 -1 O GLY B 40 N ALA B 105 SHEET 5 BC 6 GLU B 51 HIS B 57 -1 O GLU B 51 N ARG B 43 SHEET 6 BC 6 SER B 63 TYR B 67 -1 O TYR B 66 N CYS B 55 SHEET 1 BD 2 THR B 117 ALA B 118 0 SHEET 2 BD 2 ALA B 100 THR B 106 -1 N THR B 106 O THR B 117 SSBOND 1 CYS B 23 CYS B 104 1555 1555 2.03 SSBOND 2 CYS B 55 CYS B 110 1555 1555 2.19 CISPEP 1 LYS A 166 PRO A 167 0 -2.71 SITE 1 AC1 5 PRO A 167 ILE A 198 SER A 199 HIS A 200 SITE 2 AC1 5 TYR A 201 SITE 1 AC2 7 ILE A 278 PRO A 279 PRO A 280 HIS A 289 SITE 2 AC2 7 HOH A2105 ARG B 20 HOH B2066 SITE 1 AC3 4 GLY A 30 THR A 32 ARG A 41 HOH B2002 SITE 1 AC4 11 ALA A 47 ALA A 67 LYS A 69 GLU A 85 SITE 2 AC4 11 THR A 123 GLU A 124 CYS A 126 GLY A 128 SITE 3 AC4 11 LEU A 180 CYS A 190 HOH A2043 CRYST1 156.866 37.430 76.010 90.00 108.48 90.00 C 1 2 1 4 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 0.006375 0.000000 0.002131 0.00000 SCALE2 0.000000 0.026717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013871 0.00000