HEADER SUGAR BINDING PROTEIN 07-JUL-21 7RCM TITLE CRYSTAL STRUCTURE OF ADP-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, ADP, DISULFIDE, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.G.WHITBY REVDAT 3 18-OCT-23 7RCM 1 REMARK REVDAT 2 06-OCT-21 7RCM 1 JRNL REVDAT 1 29-SEP-21 7RCM 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 65530 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 3072 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4330 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.3440 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 : 118 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : -1.03000 REMARK 3 B33 (A**2) : 3.34000 REMARK 3 B12 (A**2) : -0.51000 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.785 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6143 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5708 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8356 ; 1.680 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13195 ; 1.310 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 786 ; 7.726 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 322 ;29.880 ;20.311 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 977 ;17.052 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 62 ;18.303 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 791 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6962 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1302 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): 23.8212 -38.5714 0.6585 REMARK 3 T TENSOR REMARK 3 T11: 0.3298 T22: 0.1105 REMARK 3 T33: 0.2794 T12: 0.1448 REMARK 3 T13: 0.0090 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 2.6694 L22: 1.3017 REMARK 3 L33: 1.4843 L12: -1.0408 REMARK 3 L13: 1.0763 L23: -0.6754 REMARK 3 S TENSOR REMARK 3 S11: -0.0395 S12: 0.0996 S13: -0.0975 REMARK 3 S21: -0.1223 S22: 0.0237 S23: -0.1514 REMARK 3 S31: 0.2332 S32: 0.2527 S33: 0.0157 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 : B 2 B 401 REMARK 3 ORIGIN FOR THE GROUP (A): 4.8067 -29.6254 28.9216 REMARK 3 T TENSOR REMARK 3 T11: 0.2871 T22: 0.0300 REMARK 3 T33: 0.3073 T12: 0.0100 REMARK 3 T13: -0.1368 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 1.2408 L22: 3.2123 REMARK 3 L33: 2.2779 L12: -0.2786 REMARK 3 L13: 0.4490 L23: -1.4034 REMARK 3 S TENSOR REMARK 3 S11: 0.1864 S12: -0.1579 S13: -0.1327 REMARK 3 S21: -0.0552 S22: 0.0582 S23: 0.4967 REMARK 3 S31: 0.6235 S32: -0.0302 S33: -0.2446 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7RCM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-13 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) : 1.1533 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68728 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 39.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 16.70 REMARK 200 R MERGE (I) : 0.21800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 1.13600 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 REMARK 200 STARTING MODEL: 1WUU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 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 80.21733 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 160.43467 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 120.32600 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 200.54333 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 40.10867 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 80.21733 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 160.43467 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 200.54333 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 120.32600 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 40.10867 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: 5620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 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 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 O HOH A 577 O HOH A 604 1.56 REMARK 500 O HOH B 629 O HOH B 631 1.82 REMARK 500 O HOH B 501 O HOH B 545 2.00 REMARK 500 O HOH B 548 O HOH B 626 2.07 REMARK 500 O TYR B 116 O HOH B 501 2.12 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 O HOH A 604 O HOH B 605 5554 2.11 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 ALA A 95 -78.59 -53.81 REMARK 500 SER A 140 48.96 74.57 REMARK 500 SER A 230 36.68 -91.59 REMARK 500 ALA A 232 -62.33 -101.17 REMARK 500 LEU B 213 68.96 -116.59 REMARK 500 ASN B 226 29.27 46.21 REMARK 500 SER B 230 43.93 -97.43 REMARK 500 ALA B 232 -103.97 -47.04 REMARK 500 SER B 233 52.31 -69.79 REMARK 500 SER B 234 -56.36 -129.14 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 SER A 230 LEU A 231 147.36 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 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 142 OG REMARK 620 2 ADP A 401 O2B 75.3 REMARK 620 3 ADP A 401 O2A 78.1 74.6 REMARK 620 4 HOH A 501 O 64.0 92.4 142.0 REMARK 620 5 HOH A 536 O 135.1 79.9 129.7 80.6 REMARK 620 6 HOH A 545 O 89.1 163.0 95.9 86.7 116.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 407 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 369 O REMARK 620 2 GLN A 369 OE1 77.7 REMARK 620 3 TYR A 372 O 83.4 113.2 REMARK 620 4 GLY A 374 O 139.6 83.7 71.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 142 OG REMARK 620 2 ADP B 401 O1B 93.4 REMARK 620 3 ADP B 401 O1A 96.5 85.5 REMARK 620 4 HOH B 511 O 91.8 173.6 90.2 REMARK 620 5 HOH B 579 O 71.4 95.5 167.9 89.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 408 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 369 O REMARK 620 2 TYR B 372 O 85.3 REMARK 620 3 GLY B 374 O 146.0 77.2 REMARK 620 N 1 2 DBREF 7RCM A 1 392 UNP P51570 GALK1_HUMAN 1 392 DBREF 7RCM B 1 392 UNP P51570 GALK1_HUMAN 1 392 SEQADV 7RCM ALA A 252 UNP P51570 LYS 252 ENGINEERED MUTATION SEQADV 7RCM ALA A 253 UNP P51570 GLU 253 ENGINEERED MUTATION SEQADV 7RCM ALA B 252 UNP P51570 LYS 252 ENGINEERED MUTATION SEQADV 7RCM 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 ADP A 401 27 HET GLA A 402 12 HET PO4 A 403 5 HET PO4 A 404 5 HET PO4 A 405 5 HET MG A 406 1 HET NA A 407 1 HET ADP B 401 27 HET GLA B 402 12 HET PO4 B 403 5 HET PO4 B 404 5 HET PO4 B 405 5 HET MG B 406 1 HET GOL B 407 6 HET NA B 408 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 GLA 2(C6 H12 O6) FORMUL 5 PO4 6(O4 P 3-) FORMUL 8 MG 2(MG 2+) FORMUL 9 NA 2(NA 1+) FORMUL 16 GOL C3 H8 O3 FORMUL 18 HOH *249(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 TRP A 106 5 3 HELIX 4 AA4 ALA A 107 TYR A 116 1 10 HELIX 5 AA5 SER A 140 CYS A 157 1 18 HELIX 6 AA6 THR A 162 ALA A 178 1 17 HELIX 7 AA7 ILE A 184 GLY A 193 1 10 HELIX 8 AA8 LEU A 231 LEU A 250 1 20 HELIX 9 AA9 SER A 254 VAL A 258 5 5 HELIX 10 AB1 GLN A 259 ALA A 265 1 7 HELIX 11 AB2 ALA A 266 VAL A 270 5 5 HELIX 12 AB3 SER A 271 ARG A 297 1 27 HELIX 13 AB4 ASP A 299 ASP A 317 1 19 HELIX 14 AB5 CYS A 322 ALA A 334 1 13 HELIX 15 AB6 ALA A 360 HIS A 371 1 12 HELIX 16 AB7 GLN B 8 GLY B 25 1 18 HELIX 17 AB8 THR B 45 GLN B 49 5 5 HELIX 18 AB9 PRO B 104 TRP B 106 5 3 HELIX 19 AC1 ALA B 107 TYR B 117 1 11 HELIX 20 AC2 SER B 140 CYS B 157 1 18 HELIX 21 AC3 THR B 162 ALA B 178 1 17 HELIX 22 AC4 ILE B 184 GLY B 193 1 10 HELIX 23 AC5 LEU B 231 LEU B 250 1 20 HELIX 24 AC6 SER B 254 VAL B 258 5 5 HELIX 25 AC7 GLN B 259 ALA B 266 1 8 HELIX 26 AC8 ARG B 267 VAL B 270 5 4 HELIX 27 AC9 SER B 271 GLY B 298 1 28 HELIX 28 AD1 ASP B 299 ASP B 317 1 19 HELIX 29 AD2 CYS B 322 ALA B 334 1 13 HELIX 30 AD3 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 VAL A 129 N LEU A 76 SHEET 4 AA1 6 PRO A 54 PRO A 67 -1 N VAL A 64 O VAL A 128 SHEET 5 AA1 6 LEU A 30 ASN A 39 -1 N LEU A 30 O GLY A 65 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 LEU A 221 O THR A 354 SHEET 4 AA3 4 THR A 377 SER A 381 -1 O THR A 377 N ASN A 224 SHEET 1 AA4 6 ARG B 87 PRO B 91 0 SHEET 2 AA4 6 LEU B 72 THR B 77 -1 N VAL B 73 O PHE B 90 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 LEU B 30 O GLY B 65 SHEET 6 AA4 6 LYS B 388 LEU B 390 -1 O LEU B 390 N ALA B 31 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 LEU B 221 O THR B 354 SHEET 4 AA5 4 THR B 377 SER B 381 -1 O TYR B 379 N ILE B 222 SSBOND 1 CYS A 391 CYS B 391 1555 1555 2.08 LINK OG SER A 142 MG MG A 406 1555 1555 2.63 LINK O GLN A 369 NA NA A 407 1555 1555 2.45 LINK OE1 GLN A 369 NA NA A 407 1555 1555 2.97 LINK O TYR A 372 NA NA A 407 1555 1555 2.69 LINK O GLY A 374 NA NA A 407 1555 1555 2.65 LINK O2B ADP A 401 MG MG A 406 1555 1555 2.44 LINK O2A ADP A 401 MG MG A 406 1555 1555 2.67 LINK MG MG A 406 O HOH A 501 1555 1555 2.43 LINK MG MG A 406 O HOH A 536 1555 1555 2.81 LINK MG MG A 406 O HOH A 545 1555 1555 2.58 LINK OG SER B 142 MG MG B 406 1555 1555 2.44 LINK O GLN B 369 NA NA B 408 1555 1555 2.35 LINK O TYR B 372 NA NA B 408 1555 1555 2.66 LINK O GLY B 374 NA NA B 408 1555 1555 2.68 LINK O1B ADP B 401 MG MG B 406 1555 1555 2.44 LINK O1A ADP B 401 MG MG B 406 1555 1555 2.38 LINK MG MG B 406 O HOH B 511 1555 1555 2.61 LINK MG MG B 406 O HOH B 579 1555 1555 2.53 CISPEP 1 GLU A 84 PRO A 85 0 -4.62 CISPEP 2 THR A 103 PRO A 104 0 7.40 CISPEP 3 ALA A 120 PRO A 121 0 -5.53 CISPEP 4 GLU B 84 PRO B 85 0 -1.33 CISPEP 5 THR B 103 PRO B 104 0 0.39 CISPEP 6 ALA B 120 PRO B 121 0 -4.47 CRYST1 128.793 128.793 240.652 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 0.007764 0.004483 0.000000 0.00000 SCALE2 0.000000 0.008966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004155 0.00000