HEADER TRANSFERASE/INHIBITOR 08-SEP-21 7S4C TITLE CRYSTAL STRUCTURE OF INHIBITOR-BOUND GALACTOKINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALACTOKINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GALACTOSE KINASE; COMPND 5 EC: 2.7.1.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GALK1, GALK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS174; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21D KEYWDS GALK, GALACTOKINASE, GALACTOSE, INHIBITOR, DISULFIDE, SUGAR BINDING KEYWDS 2 PROTEIN, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.G.WHITBY REVDAT 3 18-OCT-23 7S4C 1 REMARK REVDAT 2 06-OCT-21 7S4C 1 JRNL REVDAT 1 29-SEP-21 7S4C 0 JRNL AUTH L.LIU,M.TANG,R.PRAGANI,F.G.WHITBY,Y.Q.ZHANG,B.BALAKRISHNAN, JRNL AUTH 2 Y.FANG,S.KARAVADHI,D.TAO,C.A.LECLAIR,M.D.HALL,J.J.MARUGAN, JRNL AUTH 3 M.BOXER,M.SHEN,C.P.HILL,K.LAI,S.PATNAIK JRNL TITL STRUCTURE-BASED OPTIMIZATION OF SMALL MOLECULE HUMAN JRNL TITL 2 GALACTOKINASE INHIBITORS. JRNL REF J.MED.CHEM. V. 64 13551 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34491744 JRNL DOI 10.1021/ACS.JMEDCHEM.1C00945 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 58715 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2268 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4125 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 156 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5900 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 157 REMARK 3 SOLVENT ATOMS : 476 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.18000 REMARK 3 B22 (A**2) : -1.18000 REMARK 3 B33 (A**2) : 3.82000 REMARK 3 B12 (A**2) : -0.59000 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): 0.176 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.062 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6181 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5972 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8402 ; 1.759 ; 1.670 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13518 ; 0.807 ; 1.581 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 782 ; 7.600 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 322 ;28.963 ;20.311 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 977 ;16.921 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 62 ;21.449 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 782 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7127 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1448 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 392 REMARK 3 RESIDUE RANGE : A 401 A 403 REMARK 3 ORIGIN FOR THE GROUP (A): 24.525 -38.285 0.681 REMARK 3 T TENSOR REMARK 3 T11: 0.2491 T22: 0.1187 REMARK 3 T33: 0.0206 T12: 0.0947 REMARK 3 T13: -0.0146 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 3.0214 L22: 0.9505 REMARK 3 L33: 1.3781 L12: -1.1698 REMARK 3 L13: 1.3378 L23: -0.9176 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: 0.0997 S13: 0.0368 REMARK 3 S21: -0.1316 S22: -0.0148 S23: -0.0941 REMARK 3 S31: 0.1667 S32: 0.2264 S33: 0.0635 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 392 REMARK 3 RESIDUE RANGE : B 401 B 402 REMARK 3 ORIGIN FOR THE GROUP (A): 5.352 -29.425 28.977 REMARK 3 T TENSOR REMARK 3 T11: 0.2347 T22: 0.0488 REMARK 3 T33: 0.2909 T12: -0.0025 REMARK 3 T13: -0.0681 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 1.0499 L22: 3.9292 REMARK 3 L33: 2.4808 L12: -0.4923 REMARK 3 L13: 0.3823 L23: -1.8437 REMARK 3 S TENSOR REMARK 3 S11: 0.1555 S12: -0.1250 S13: -0.0668 REMARK 3 S21: -0.1286 S22: 0.1608 S23: 0.8968 REMARK 3 S31: 0.5572 S32: -0.1764 S33: -0.3162 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7S4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61072 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 21.00 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.3000 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) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.89300 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: PHASER 2.5.6 REMARK 200 STARTING MODEL: 1WUU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEEDING INTO DROPS CONTAINING GALK REMARK 280 PROTEIN AT 8 MG/ML, 2.3M NA/K PH6.8, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 286K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 80.26300 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 160.52600 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 120.39450 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 200.65750 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 40.13150 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 80.26300 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 160.52600 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 200.65750 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 120.39450 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 40.13150 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: 3530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 527 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 MET B 1 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 HH12 ARG B 18 OE1 GLU B 235 5554 1.56 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 11 CD GLU A 11 OE1 0.097 REMARK 500 GLU B 23 CD GLU B 23 OE1 0.087 REMARK 500 GLU B 84 CD GLU B 84 OE2 0.068 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 21 NE - CZ - NH1 ANGL. DEV. = 3.6 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 LYS A 195 129.96 -36.85 REMARK 500 HIS A 229 173.33 -58.11 REMARK 500 LEU A 231 -2.08 -157.27 REMARK 500 SER A 233 -59.85 -24.14 REMARK 500 SER A 234 -70.16 -109.36 REMARK 500 ARG B 97 114.08 -160.22 REMARK 500 HIS B 229 172.45 -56.08 REMARK 500 SER B 233 -66.64 -20.47 REMARK 500 SER B 234 -77.37 -81.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 232 SER A 233 143.44 REMARK 500 SER A 233 SER A 234 -149.33 REMARK 500 ALA B 232 SER B 233 145.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 768 DISTANCE = 7.23 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 369 O REMARK 620 2 GLN A 369 OE1 78.5 REMARK 620 3 TYR A 372 O 85.4 117.9 REMARK 620 4 GLY A 374 O 140.2 86.5 69.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 369 O REMARK 620 2 GLN B 369 OE1 60.2 REMARK 620 3 TYR B 372 O 83.3 135.2 REMARK 620 4 GLY B 374 O 129.8 98.3 85.1 REMARK 620 5 HOH B 551 O 57.0 83.7 98.3 172.9 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7S49 RELATED DB: PDB REMARK 900 RELATED ID: 7RCM RELATED DB: PDB REMARK 900 RELATED ID: 7RCL RELATED DB: PDB DBREF 7S4C A 1 392 UNP P51570 GALK1_HUMAN 1 392 DBREF 7S4C B 1 392 UNP P51570 GALK1_HUMAN 1 392 SEQADV 7S4C ALA A 252 UNP P51570 LYS 252 ENGINEERED MUTATION SEQADV 7S4C ALA A 253 UNP P51570 GLU 253 ENGINEERED MUTATION SEQADV 7S4C ALA B 252 UNP P51570 LYS 252 ENGINEERED MUTATION SEQADV 7S4C ALA B 253 UNP P51570 GLU 253 ENGINEERED MUTATION SEQRES 1 A 392 MET ALA ALA LEU ARG GLN PRO GLN VAL ALA GLU LEU LEU SEQRES 2 A 392 ALA GLU ALA ARG ARG ALA PHE ARG GLU GLU PHE GLY ALA SEQRES 3 A 392 GLU PRO GLU LEU ALA VAL SER ALA PRO GLY ARG VAL ASN SEQRES 4 A 392 LEU ILE GLY GLU HIS THR ASP TYR ASN GLN GLY LEU VAL SEQRES 5 A 392 LEU PRO MET ALA LEU GLU LEU MET THR VAL LEU VAL GLY SEQRES 6 A 392 SER PRO ARG LYS ASP GLY LEU VAL SER LEU LEU THR THR SEQRES 7 A 392 SER GLU GLY ALA ASP GLU PRO GLN ARG LEU GLN PHE PRO SEQRES 8 A 392 LEU PRO THR ALA GLN ARG SER LEU GLU PRO GLY THR PRO SEQRES 9 A 392 ARG TRP ALA ASN TYR VAL LYS GLY VAL ILE GLN TYR TYR SEQRES 10 A 392 PRO ALA ALA PRO LEU PRO GLY PHE SER ALA VAL VAL VAL SEQRES 11 A 392 SER SER VAL PRO LEU GLY GLY GLY LEU SER SER SER ALA SEQRES 12 A 392 SER LEU GLU VAL ALA THR TYR THR PHE LEU GLN GLN LEU SEQRES 13 A 392 CYS PRO ASP SER GLY THR ILE ALA ALA ARG ALA GLN VAL SEQRES 14 A 392 CYS GLN GLN ALA GLU HIS SER PHE ALA GLY MET PRO CYS SEQRES 15 A 392 GLY ILE MET ASP GLN PHE ILE SER LEU MET GLY GLN LYS SEQRES 16 A 392 GLY HIS ALA LEU LEU ILE ASP CYS ARG SER LEU GLU THR SEQRES 17 A 392 SER LEU VAL PRO LEU SER ASP PRO LYS LEU ALA VAL LEU SEQRES 18 A 392 ILE THR ASN SER ASN VAL ARG HIS SER LEU ALA SER SER SEQRES 19 A 392 GLU TYR PRO VAL ARG ARG ARG GLN CYS GLU GLU VAL ALA SEQRES 20 A 392 ARG ALA LEU GLY ALA ALA SER LEU ARG GLU VAL GLN LEU SEQRES 21 A 392 GLU GLU LEU GLU ALA ALA ARG ASP LEU VAL SER LYS GLU SEQRES 22 A 392 GLY PHE ARG ARG ALA ARG HIS VAL VAL GLY GLU ILE ARG SEQRES 23 A 392 ARG THR ALA GLN ALA ALA ALA ALA LEU ARG ARG GLY ASP SEQRES 24 A 392 TYR ARG ALA PHE GLY ARG LEU MET VAL GLU SER HIS ARG SEQRES 25 A 392 SER LEU ARG ASP ASP TYR GLU VAL SER CYS PRO GLU LEU SEQRES 26 A 392 ASP GLN LEU VAL GLU ALA ALA LEU ALA VAL PRO GLY VAL SEQRES 27 A 392 TYR GLY SER ARG MET THR GLY GLY GLY PHE GLY GLY CYS SEQRES 28 A 392 THR VAL THR LEU LEU GLU ALA SER ALA ALA PRO HIS ALA SEQRES 29 A 392 MET ARG HIS ILE GLN GLU HIS TYR GLY GLY THR ALA THR SEQRES 30 A 392 PHE TYR LEU SER GLN ALA ALA ASP GLY ALA LYS VAL LEU SEQRES 31 A 392 CYS LEU SEQRES 1 B 392 MET ALA ALA LEU ARG GLN PRO GLN VAL ALA GLU LEU LEU SEQRES 2 B 392 ALA GLU ALA ARG ARG ALA PHE ARG GLU GLU PHE GLY ALA SEQRES 3 B 392 GLU PRO GLU LEU ALA VAL SER ALA PRO GLY ARG VAL ASN SEQRES 4 B 392 LEU ILE GLY GLU HIS THR ASP TYR ASN GLN GLY LEU VAL SEQRES 5 B 392 LEU PRO MET ALA LEU GLU LEU MET THR VAL LEU VAL GLY SEQRES 6 B 392 SER PRO ARG LYS ASP GLY LEU VAL SER LEU LEU THR THR SEQRES 7 B 392 SER GLU GLY ALA ASP GLU PRO GLN ARG LEU GLN PHE PRO SEQRES 8 B 392 LEU PRO THR ALA GLN ARG SER LEU GLU PRO GLY THR PRO SEQRES 9 B 392 ARG TRP ALA ASN TYR VAL LYS GLY VAL ILE GLN TYR TYR SEQRES 10 B 392 PRO ALA ALA PRO LEU PRO GLY PHE SER ALA VAL VAL VAL SEQRES 11 B 392 SER SER VAL PRO LEU GLY GLY GLY LEU SER SER SER ALA SEQRES 12 B 392 SER LEU GLU VAL ALA THR TYR THR PHE LEU GLN GLN LEU SEQRES 13 B 392 CYS PRO ASP SER GLY THR ILE ALA ALA ARG ALA GLN VAL SEQRES 14 B 392 CYS GLN GLN ALA GLU HIS SER PHE ALA GLY MET PRO CYS SEQRES 15 B 392 GLY ILE MET ASP GLN PHE ILE SER LEU MET GLY GLN LYS SEQRES 16 B 392 GLY HIS ALA LEU LEU ILE ASP CYS ARG SER LEU GLU THR SEQRES 17 B 392 SER LEU VAL PRO LEU SER ASP PRO LYS LEU ALA VAL LEU SEQRES 18 B 392 ILE THR ASN SER ASN VAL ARG HIS SER LEU ALA SER SER SEQRES 19 B 392 GLU TYR PRO VAL ARG ARG ARG GLN CYS GLU GLU VAL ALA SEQRES 20 B 392 ARG ALA LEU GLY ALA ALA SER LEU ARG GLU VAL GLN LEU SEQRES 21 B 392 GLU GLU LEU GLU ALA ALA ARG ASP LEU VAL SER LYS GLU SEQRES 22 B 392 GLY PHE ARG ARG ALA ARG HIS VAL VAL GLY GLU ILE ARG SEQRES 23 B 392 ARG THR ALA GLN ALA ALA ALA ALA LEU ARG ARG GLY ASP SEQRES 24 B 392 TYR ARG ALA PHE GLY ARG LEU MET VAL GLU SER HIS ARG SEQRES 25 B 392 SER LEU ARG ASP ASP TYR GLU VAL SER CYS PRO GLU LEU SEQRES 26 B 392 ASP GLN LEU VAL GLU ALA ALA LEU ALA VAL PRO GLY VAL SEQRES 27 B 392 TYR GLY SER ARG MET THR GLY GLY GLY PHE GLY GLY CYS SEQRES 28 B 392 THR VAL THR LEU LEU GLU ALA SER ALA ALA PRO HIS ALA SEQRES 29 B 392 MET ARG HIS ILE GLN GLU HIS TYR GLY GLY THR ALA THR SEQRES 30 B 392 PHE TYR LEU SER GLN ALA ALA ASP GLY ALA LYS VAL LEU SEQRES 31 B 392 CYS LEU HET GLA A 401 24 HET V3V A 402 54 HET V3V A 403 54 HET NA A 404 1 HET PO4 A 405 5 HET PO4 A 406 5 HET PO4 A 407 5 HET GLA B 401 24 HET V3V B 402 54 HET NA B 403 1 HET PO4 B 404 5 HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM V3V 2-({(4R)-4-(2-CHLOROPHENYL)-2-[(6-FLUORO-1,3- HETNAM 2 V3V BENZOXAZOL-2-YL)AMINO]-6-METHYL-1,4-DIHYDROPYRIMIDINE- HETNAM 3 V3V 5-CARBONYL}AMINO)PYRIDINE-4-CARBOXYLIC ACID HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE FORMUL 3 GLA 2(C6 H12 O6) FORMUL 4 V3V 3(C25 H18 CL F N6 O4) FORMUL 6 NA 2(NA 1+) FORMUL 7 PO4 4(O4 P 3-) FORMUL 14 HOH *476(H2 O) HELIX 1 AA1 GLN A 8 GLY A 25 1 18 HELIX 2 AA2 THR A 45 GLN A 49 5 5 HELIX 3 AA3 PRO A 104 TYR A 116 1 13 HELIX 4 AA4 SER A 140 CYS A 157 1 18 HELIX 5 AA5 THR A 162 ALA A 178 1 17 HELIX 6 AA6 ILE A 184 GLY A 193 1 10 HELIX 7 AA7 SER A 234 LEU A 250 1 17 HELIX 8 AA8 SER A 254 VAL A 258 5 5 HELIX 9 AA9 GLN A 259 ALA A 265 1 7 HELIX 10 AB1 ALA A 266 VAL A 270 5 5 HELIX 11 AB2 SER A 271 ARG A 297 1 27 HELIX 12 AB3 ASP A 299 ASP A 317 1 19 HELIX 13 AB4 CYS A 322 ALA A 334 1 13 HELIX 14 AB5 ALA A 360 HIS A 371 1 12 HELIX 15 AB6 GLN B 8 GLY B 25 1 18 HELIX 16 AB7 THR B 45 GLN B 49 5 5 HELIX 17 AB8 PRO B 104 TYR B 117 1 14 HELIX 18 AB9 SER B 140 CYS B 157 1 18 HELIX 19 AC1 THR B 162 ALA B 178 1 17 HELIX 20 AC2 ILE B 184 GLY B 193 1 10 HELIX 21 AC3 SER B 230 LEU B 250 1 21 HELIX 22 AC4 SER B 254 VAL B 258 5 5 HELIX 23 AC5 GLN B 259 ALA B 266 1 8 HELIX 24 AC6 ARG B 267 VAL B 270 5 4 HELIX 25 AC7 SER B 271 ARG B 297 1 27 HELIX 26 AC8 ASP B 299 ASP B 317 1 19 HELIX 27 AC9 CYS B 322 ALA B 334 1 13 HELIX 28 AD1 ALA B 360 HIS B 371 1 12 SHEET 1 AA1 6 ARG A 87 PRO A 91 0 SHEET 2 AA1 6 LEU A 72 THR A 77 -1 N LEU A 75 O LEU A 88 SHEET 3 AA1 6 PHE A 125 SER A 131 1 O PHE A 125 N SER A 74 SHEET 4 AA1 6 PRO A 54 PRO A 67 -1 N VAL A 62 O VAL A 130 SHEET 5 AA1 6 LEU A 30 ASN A 39 -1 N ALA A 34 O THR A 61 SHEET 6 AA1 6 LYS A 388 LEU A 390 -1 O LEU A 390 N ALA A 31 SHEET 1 AA2 6 LEU A 51 VAL A 52 0 SHEET 2 AA2 6 HIS A 197 ASP A 202 -1 O ILE A 201 N VAL A 52 SHEET 3 AA2 6 THR A 208 PRO A 212 -1 O VAL A 211 N ALA A 198 SHEET 4 AA2 6 THR B 208 PRO B 212 -1 O THR B 208 N LEU A 210 SHEET 5 AA2 6 HIS B 197 ASP B 202 -1 N LEU B 200 O SER B 209 SHEET 6 AA2 6 LEU B 51 VAL B 52 -1 N VAL B 52 O ILE B 201 SHEET 1 AA3 4 VAL A 338 MET A 343 0 SHEET 2 AA3 4 GLY A 349 GLU A 357 -1 O LEU A 355 N TYR A 339 SHEET 3 AA3 4 LEU A 218 ARG A 228 -1 N ALA A 219 O LEU A 356 SHEET 4 AA3 4 THR A 377 LEU A 380 -1 O TYR A 379 N ILE A 222 SHEET 1 AA4 6 ARG B 87 PRO B 91 0 SHEET 2 AA4 6 LEU B 72 THR B 77 -1 N LEU B 75 O LEU B 88 SHEET 3 AA4 6 PHE B 125 SER B 131 1 O VAL B 129 N LEU B 76 SHEET 4 AA4 6 PRO B 54 PRO B 67 -1 N VAL B 62 O VAL B 130 SHEET 5 AA4 6 LEU B 30 ASN B 39 -1 N ALA B 34 O THR B 61 SHEET 6 AA4 6 LYS B 388 VAL B 389 -1 O LYS B 388 N SER B 33 SHEET 1 AA5 4 VAL B 338 MET B 343 0 SHEET 2 AA5 4 GLY B 349 GLU B 357 -1 O VAL B 353 N ARG B 342 SHEET 3 AA5 4 LEU B 218 ARG B 228 -1 N ALA B 219 O LEU B 356 SHEET 4 AA5 4 THR B 377 LEU B 380 -1 O THR B 377 N ASN B 224 SSBOND 1 CYS A 391 CYS B 391 1555 1555 2.02 LINK O GLN A 369 NA NA A 404 1555 1555 2.58 LINK OE1 GLN A 369 NA NA A 404 1555 1555 2.90 LINK O TYR A 372 NA NA A 404 1555 1555 2.74 LINK O GLY A 374 NA NA A 404 1555 1555 2.51 LINK O GLN B 369 NA NA B 403 1555 1555 2.84 LINK OE1 GLN B 369 NA NA B 403 1555 1555 2.09 LINK O TYR B 372 NA NA B 403 1555 1555 2.37 LINK O GLY B 374 NA NA B 403 1555 1555 2.62 LINK NA NA B 403 O HOH B 551 1555 1555 2.75 CISPEP 1 GLU A 84 PRO A 85 0 -4.35 CISPEP 2 THR A 103 PRO A 104 0 -3.30 CISPEP 3 ALA A 120 PRO A 121 0 -3.79 CISPEP 4 GLU B 84 PRO B 85 0 2.91 CISPEP 5 THR B 103 PRO B 104 0 0.73 CISPEP 6 ALA B 120 PRO B 121 0 -4.05 CRYST1 129.216 129.216 240.789 90.00 90.00 120.00 P 61 2 2 24 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 0.007739 0.004468 0.000000 0.00000 SCALE2 0.000000 0.008936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004153 0.00000