HEADER TRANSFERASE 14-APR-09 3H1V TITLE HUMAN GLUCOKINASE IN COMPLEX WITH A SYNTHETIC ACTIVATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOKINASE; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: UNP RESIDUES 16-465; COMPND 5 SYNONYM: HEXOKINASE TYPE IV, HK IV, HEXOKINASE-4, HK4, HEXOKINASE-D; COMPND 6 EC: 2.7.1.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GCK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5ALFA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFLAG-CTC KEYWDS GLUCOKINASE, DIABETES, ALLOSTERIC ACTIVATOR, ALTERNATIVE SPLICING, KEYWDS 2 ATP-BINDING, DIABETES MELLITUS, DISEASE MUTATION, GLYCOLYSIS, KEYWDS 3 KINASE, NUCLEOTIDE-BINDING, POLYMORPHISM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KAMATA,K.TAKAHASHI REVDAT 4 20-MAR-24 3H1V 1 HETSYN REVDAT 3 29-JUL-20 3H1V 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 SITE REVDAT 2 01-NOV-17 3H1V 1 REMARK REVDAT 1 06-OCT-09 3H1V 0 JRNL AUTH K.TAKAHASHI,N.HASHIMOTO,C.NAKAMA,K.KAMATA,K.SASAKI, JRNL AUTH 2 R.YOSHIMOTO,S.OHYAMA,H.HOSAKA,H.MARUKI,Y.NAGATA,J.EIKI, JRNL AUTH 3 T.NISHIMURA JRNL TITL THE DESIGN AND OPTIMIZATION OF A SERIES OF JRNL TITL 2 2-(PYRIDIN-2-YL)-1H-BENZIMIDAZOLE COMPOUNDS AS ALLOSTERIC JRNL TITL 3 GLUCOKINASE ACTIVATORS. JRNL REF BIOORG.MED.CHEM. V. 17 7042 2009 JRNL REFN ISSN 0968-0896 JRNL PMID 19736020 JRNL DOI 10.1016/J.BMC.2009.05.037 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 34816 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1733 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) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2011 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.226 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.413 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3596 ; 0.023 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4839 ; 2.013 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 445 ; 6.313 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;38.942 ;24.035 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 658 ;19.052 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;21.354 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 529 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2751 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1861 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 79 ; 0.441 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2461 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 123 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 8 ; 0.342 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.290 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 39 ; 0.443 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.251 ; 0.200 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): 2200 ; 1.322 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3529 ; 2.338 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1430 ; 3.483 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1310 ; 5.453 ; 4.500 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 : NULL 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 3H1V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052586. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34817 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.29200 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 1500, HEPES, PH 6.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 217.41600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.70800 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 163.06200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 54.35400 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 271.77000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 217.41600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 108.70800 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 54.35400 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 163.06200 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 271.77000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 CYS X 461 REMARK 465 MET X 462 REMARK 465 LEU X 463 REMARK 465 GLY X 464 REMARK 465 GLN X 465 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 X 349 NH2 ARG X 358 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU X 421 OE2 GLU X 421 11655 1.29 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 ASP X 205 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG X 368 NE - CZ - NH1 ANGL. DEV. = 3.2 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 THR X 65 149.95 75.70 REMARK 500 GLU X 67 58.30 -69.18 REMARK 500 GLU X 95 -80.56 -71.20 REMARK 500 LYS X 136 -0.46 -57.52 REMARK 500 MET X 139 17.42 -140.71 REMARK 500 SER X 151 58.10 -92.65 REMARK 500 LYS X 172 3.89 -155.63 REMARK 500 LEU X 184 -38.05 -37.94 REMARK 500 LYS X 190 -71.02 -59.52 REMARK 500 ARG X 191 19.38 -54.76 REMARK 500 ASP X 194 -85.30 -18.24 REMARK 500 ASP X 217 99.98 -162.62 REMARK 500 ASP X 400 -76.35 -68.33 REMARK 500 CYS X 457 47.04 -93.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 3H1V X 16 465 UNP P35557 HXK4_HUMAN 16 465 SEQADV 3H1V MET X 15 UNP P35557 INITIATING METHIONINE SEQRES 1 X 451 MET VAL GLU GLN ILE LEU ALA GLU PHE GLN LEU GLN GLU SEQRES 2 X 451 GLU ASP LEU LYS LYS VAL MET ARG ARG MET GLN LYS GLU SEQRES 3 X 451 MET ASP ARG GLY LEU ARG LEU GLU THR HIS GLU GLU ALA SEQRES 4 X 451 SER VAL LYS MET LEU PRO THR TYR VAL ARG SER THR PRO SEQRES 5 X 451 GLU GLY SER GLU VAL GLY ASP PHE LEU SER LEU ASP LEU SEQRES 6 X 451 GLY GLY THR ASN PHE ARG VAL MET LEU VAL LYS VAL GLY SEQRES 7 X 451 GLU GLY GLU GLU GLY GLN TRP SER VAL LYS THR LYS HIS SEQRES 8 X 451 GLN MET TYR SER ILE PRO GLU ASP ALA MET THR GLY THR SEQRES 9 X 451 ALA GLU MET LEU PHE ASP TYR ILE SER GLU CYS ILE SER SEQRES 10 X 451 ASP PHE LEU ASP LYS HIS GLN MET LYS HIS LYS LYS LEU SEQRES 11 X 451 PRO LEU GLY PHE THR PHE SER PHE PRO VAL ARG HIS GLU SEQRES 12 X 451 ASP ILE ASP LYS GLY ILE LEU LEU ASN TRP THR LYS GLY SEQRES 13 X 451 PHE LYS ALA SER GLY ALA GLU GLY ASN ASN VAL VAL GLY SEQRES 14 X 451 LEU LEU ARG ASP ALA ILE LYS ARG ARG GLY ASP PHE GLU SEQRES 15 X 451 MET ASP VAL VAL ALA MET VAL ASN ASP THR VAL ALA THR SEQRES 16 X 451 MET ILE SER CYS TYR TYR GLU ASP HIS GLN CYS GLU VAL SEQRES 17 X 451 GLY MET ILE VAL GLY THR GLY CYS ASN ALA CYS TYR MET SEQRES 18 X 451 GLU GLU MET GLN ASN VAL GLU LEU VAL GLU GLY ASP GLU SEQRES 19 X 451 GLY ARG MET CYS VAL ASN THR GLU TRP GLY ALA PHE GLY SEQRES 20 X 451 ASP SER GLY GLU LEU ASP GLU PHE LEU LEU GLU TYR ASP SEQRES 21 X 451 ARG LEU VAL ASP GLU SER SER ALA ASN PRO GLY GLN GLN SEQRES 22 X 451 LEU TYR GLU LYS LEU ILE GLY GLY LYS TYR MET GLY GLU SEQRES 23 X 451 LEU VAL ARG LEU VAL LEU LEU ARG LEU VAL ASP GLU ASN SEQRES 24 X 451 LEU LEU PHE HIS GLY GLU ALA SER GLU GLN LEU ARG THR SEQRES 25 X 451 ARG GLY ALA PHE GLU THR ARG PHE VAL SER GLN VAL GLU SEQRES 26 X 451 SER ASP THR GLY ASP ARG LYS GLN ILE TYR ASN ILE LEU SEQRES 27 X 451 SER THR LEU GLY LEU ARG PRO SER THR THR ASP CYS ASP SEQRES 28 X 451 ILE VAL ARG ARG ALA CYS GLU SER VAL SER THR ARG ALA SEQRES 29 X 451 ALA HIS MET CYS SER ALA GLY LEU ALA GLY VAL ILE ASN SEQRES 30 X 451 ARG MET ARG GLU SER ARG SER GLU ASP VAL MET ARG ILE SEQRES 31 X 451 THR VAL GLY VAL ASP GLY SER VAL TYR LYS LEU HIS PRO SEQRES 32 X 451 SER PHE LYS GLU ARG PHE HIS ALA SER VAL ARG ARG LEU SEQRES 33 X 451 THR PRO SER CYS GLU ILE THR PHE ILE GLU SER GLU GLU SEQRES 34 X 451 GLY SER GLY ARG GLY ALA ALA LEU VAL SER ALA VAL ALA SEQRES 35 X 451 CYS LYS LYS ALA CYS MET LEU GLY GLN HET GLC X 500 12 HET TK1 X 501 34 HET NA X 600 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM TK1 1-({5-[4-(METHYLSULFONYL)PHENOXY]-2-PYRIDIN-2-YL-1H- HETNAM 2 TK1 BENZIMIDAZOL-6-YL}METHYL)PYRROLIDINE-2,5-DIONE HETNAM NA SODIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC C6 H12 O6 FORMUL 3 TK1 C24 H20 N4 O5 S FORMUL 4 NA NA 1+ FORMUL 5 HOH *120(H2 O) HELIX 1 1 MET X 15 ALA X 21 1 7 HELIX 2 2 GLU X 22 GLN X 24 5 3 HELIX 3 3 GLN X 26 ARG X 46 1 21 HELIX 4 4 PRO X 111 THR X 116 1 6 HELIX 5 5 THR X 118 LYS X 136 1 19 HELIX 6 6 ASN X 180 ARG X 191 1 12 HELIX 7 7 ASN X 204 TYR X 215 1 12 HELIX 8 8 GLN X 239 VAL X 241 5 3 HELIX 9 9 GLU X 256 PHE X 260 5 5 HELIX 10 10 LEU X 271 SER X 280 1 10 HELIX 11 11 TYR X 289 ILE X 293 5 5 HELIX 12 12 TYR X 297 GLU X 312 1 16 HELIX 13 13 LEU X 315 GLU X 319 5 5 HELIX 14 14 GLU X 331 GLU X 339 1 9 HELIX 15 15 ARG X 345 THR X 354 1 10 HELIX 16 16 SER X 360 ARG X 397 1 38 HELIX 17 17 GLY X 410 HIS X 416 1 7 HELIX 18 18 SER X 418 LEU X 430 1 13 HELIX 19 19 GLU X 443 CYS X 457 1 15 SHEET 1 A 6 LEU X 58 ARG X 63 0 SHEET 2 A 6 ARG X 250 ASN X 254 -1 O CYS X 252 N VAL X 62 SHEET 3 A 6 CYS X 230 GLU X 237 -1 N GLU X 236 O MET X 251 SHEET 4 A 6 CYS X 220 VAL X 226 -1 N ILE X 225 O ASN X 231 SHEET 5 A 6 MET X 402 ASP X 409 1 O ASP X 409 N VAL X 226 SHEET 6 A 6 CYS X 434 GLU X 440 1 O GLU X 435 N MET X 402 SHEET 1 B 5 TRP X 99 SER X 109 0 SHEET 2 B 5 ASN X 83 GLY X 92 -1 N PHE X 84 O TYR X 108 SHEET 3 B 5 GLY X 72 LEU X 79 -1 N PHE X 74 O VAL X 89 SHEET 4 B 5 PRO X 145 PHE X 150 1 O PRO X 145 N LEU X 75 SHEET 5 B 5 ASP X 198 VAL X 203 1 O ASP X 198 N LEU X 146 SHEET 1 C 2 VAL X 154 ASP X 158 0 SHEET 2 C 2 LYS X 161 LEU X 164 -1 O LYS X 161 N GLU X 157 CRYST1 79.793 79.793 326.124 90.00 90.00 120.00 P 65 2 2 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 0.012532 0.007236 0.000000 0.00000 SCALE2 0.000000 0.014471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003066 0.00000