PDB Short entry for 5W2H HEADER TRANSFERASE 06-JUN-17 5W2H TITLE CRYSTAL STRUCTURE OF THE CORE CATALYTIC DOMAIN OF HUMAN INOSITOL TITLE 2 PHOSPHATE MULTIKINASE IN COMPLEX WITH INS(1,4,5)P3 AND ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL POLYPHOSPHATE MULTIKINASE,INOSITOL POLYPHOSPHATE COMPND 3 MULTIKINASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: INOSITOL 1,3,4,6-TETRAKISPHOSPHATE 5-KINASE,INOSITOL 1,3,4, COMPND 6 6-TETRAKISPHOSPHATE 5-KINASE; COMPND 7 EC: 2.7.1.151; COMPND 8 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: IPMK, IMPK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, INOSITOL, INOSITOL POLYPHOSPHATE, PHOSPHATIDYLINOSITOL, KEYWDS 2 SPECIFICITY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,S.B.SHEARS REVDAT 5 17-JAN-18 5W2H 1 REMARK DBREF SEQADV HELIX REVDAT 5 2 1 SHEET LINK SITE ATOM REVDAT 4 20-DEC-17 5W2H 1 REMARK DBREF SEQADV HELIX REVDAT 4 2 1 SHEET LINK SITE ATOM REVDAT 3 15-NOV-17 5W2H 1 JRNL REVDAT 2 20-SEP-17 5W2H 1 JRNL REVDAT 1 13-SEP-17 5W2H 0 JRNL AUTH H.WANG,S.B.SHEARS JRNL TITL STRUCTURAL FEATURES OF HUMAN INOSITOL PHOSPHATE MULTIKINASE JRNL TITL 2 RATIONALIZE ITS INOSITOL PHOSPHATE KINASE AND JRNL TITL 3 PHOSPHOINOSITIDE 3-KINASE ACTIVITIES. JRNL REF J. BIOL. CHEM. V. 292 18192 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28882892 JRNL DOI 10.1074/JBC.M117.801845 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 20189 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1082 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1276 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1935 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.256 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2170 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1988 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2974 ; 1.538 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4610 ; 0.758 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 265 ; 6.509 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;33.825 ;24.300 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 368 ;14.031 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;14.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 312 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2472 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 508 ; 0.002 ; 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): 1021 ; 1.685 ; 1.066 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1020 ; 1.685 ; 1.066 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1299 ; 2.320 ; 1.588 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1300 ; 2.323 ; 1.588 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1146 ; 2.965 ; 1.377 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1142 ; 2.963 ; 1.372 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1664 ; 3.262 ; 1.964 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2696 ; 5.122 ;10.454 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2643 ; 4.541 ;10.029 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4154 ; 2.966 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 41 ;43.630 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4223 ;13.429 ; 5.000 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 : 1 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 65 A 306 REMARK 3 RESIDUE RANGE : A 501 A 504 REMARK 3 ORIGIN FOR THE GROUP (A): 3.5028 18.0733 26.0429 REMARK 3 T TENSOR REMARK 3 T11: 0.0683 T22: 0.0517 REMARK 3 T33: 0.0462 T12: 0.0190 REMARK 3 T13: -0.0172 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 2.7351 L22: 0.8072 REMARK 3 L33: 1.4921 L12: -0.3970 REMARK 3 L13: -1.1337 L23: 0.2798 REMARK 3 S TENSOR REMARK 3 S11: -0.1658 S12: -0.1248 S13: -0.1824 REMARK 3 S21: 0.0854 S22: 0.1208 S23: -0.0127 REMARK 3 S31: 0.0171 S32: 0.0751 S33: 0.0450 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5W2H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21557 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.89700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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: 5W2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% (W/V) PEG 400, 0.1 M LI2SO4, 100 REMARK 280 MM MES IMIDANZOL BUFFER , PH 6.0, 50 MM BETA-MERCAPTOETHANOL.TO REMARK 280 OBTAIN COMPLEX STRUCTURES, THE APO CRYSTAL WERE FURTHER SOAKED REMARK 280 UNDER 35% (W/V) PEG 400, 0.1 M LI2SO4, 100 MM HEPES, PH 7.5 AT REMARK 280 298K IN THE PRESENCE OF 20 MM INS(1,4,5)P3, 10 MM MG AND 5MM ATP REMARK 280 FOR 1 DAY., VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 39.00750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.00750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.95750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.00750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.00750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.95750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.00750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.00750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.95750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.00750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.00750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.95750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: 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 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 O4 PO4 A 705 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 869 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 915 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 962 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 GLY A 50 REMARK 465 SER A 51 REMARK 465 PHE A 52 REMARK 465 THR A 53 REMARK 465 SER A 54 REMARK 465 HIS A 55 REMARK 465 GLN A 56 REMARK 465 VAL A 57 REMARK 465 ALA A 58 REMARK 465 GLY A 59 REMARK 465 HIS A 60 REMARK 465 MET A 61 REMARK 465 TYR A 62 REMARK 465 GLY A 63 REMARK 465 LYS A 64 REMARK 465 SER A 371 REMARK 465 GLN A 372 REMARK 465 GLY A 373 REMARK 465 GLY A 374 REMARK 465 SER A 375 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 NH1 ARG A 182 O HOH A 800 2.01 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 OE1 GLU A 173 OE1 GLU A 173 2555 1.07 REMARK 500 OD1 ASN A 242 NZ LYS A 244 2555 2.00 REMARK 500 O2 PO4 A 705 O3 PO4 A 705 7556 2.14 REMARK 500 CD GLU A 173 OE1 GLU A 173 2555 2.18 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 TYR A 168 87.84 -163.15 REMARK 500 ASN A 195 -165.74 -106.49 REMARK 500 ASP A 385 87.91 73.25 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 GLY A 376 GLY A 377 -135.46 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 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 385 OD1 REMARK 620 2 ASP A 385 OD2 53.0 REMARK 620 3 HOH A 859 O 80.6 81.4 REMARK 620 4 ADP A 703 O1B 88.3 89.1 168.4 REMARK 620 5 HOH A 803 O 57.8 97.7 124.5 50.0 REMARK 620 6 HOH A 849 O 101.7 150.3 78.9 107.1 76.0 REMARK 620 7 HOH A 919 O 155.9 103.6 90.8 98.0 141.2 98.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 385 OD2 REMARK 620 2 ADP A 703 O2A 96.9 REMARK 620 3 HOH A 854 O 92.1 82.4 REMARK 620 4 HOH A 903 O 82.1 174.8 92.6 REMARK 620 5 HOH A 925 O 173.6 89.3 90.2 91.8 REMARK 620 6 ADP A 703 O3B 90.6 91.6 173.6 93.5 87.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue I3P A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 705 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5W2G RELATED DB: PDB REMARK 900 RELATED ID: 5W2I RELATED DB: PDB DBREF 5W2H A 54 372 UNP Q8NFU5 IPMK_HUMAN 50 262 DBREF 5W2H A 378 416 UNP Q8NFU5 IPMK_HUMAN 378 416 SEQADV 5W2H GLY A 50 UNP Q8NFU5 EXPRESSION TAG SEQADV 5W2H SER A 51 UNP Q8NFU5 EXPRESSION TAG SEQADV 5W2H PHE A 52 UNP Q8NFU5 EXPRESSION TAG SEQADV 5W2H THR A 53 UNP Q8NFU5 EXPRESSION TAG SEQADV 5W2H A UNP Q8NFU5 ASP 61 DELETION SEQADV 5W2H A UNP Q8NFU5 LYS 62 DELETION SEQADV 5W2H A UNP Q8NFU5 VAL 63 DELETION SEQADV 5W2H A UNP Q8NFU5 GLY 64 DELETION SEQADV 5W2H GLY A 373 UNP Q8NFU5 LINKER SEQADV 5W2H GLY A 374 UNP Q8NFU5 LINKER SEQADV 5W2H SER A 375 UNP Q8NFU5 LINKER SEQADV 5W2H GLY A 376 UNP Q8NFU5 LINKER SEQADV 5W2H GLY A 377 UNP Q8NFU5 LINKER SEQRES 1 A 257 GLY SER PHE THR SER HIS GLN VAL ALA GLY HIS MET TYR SEQRES 2 A 257 GLY LYS ILE LEU GLN HIS PRO ASP GLY THR VAL LEU LYS SEQRES 3 A 257 GLN LEU GLN PRO PRO PRO ARG GLY PRO ARG GLU LEU GLU SEQRES 4 A 257 PHE TYR ASN MET VAL TYR ALA ALA ASP CYS PHE ASP GLY SEQRES 5 A 257 VAL LEU LEU GLU LEU ARG LYS TYR LEU PRO LYS TYR TYR SEQRES 6 A 257 GLY ILE TRP SER PRO PRO THR ALA PRO ASN ASP LEU TYR SEQRES 7 A 257 LEU LYS LEU GLU ASP VAL THR HIS LYS PHE ASN LYS PRO SEQRES 8 A 257 CYS ILE MET ASP VAL LYS ILE GLY GLN LYS SER TYR ASP SEQRES 9 A 257 PRO PHE ALA SER SER GLU LYS ILE GLN GLN GLN VAL SER SEQRES 10 A 257 LYS TYR PRO LEU MET GLU GLU ILE GLY PHE LEU VAL LEU SEQRES 11 A 257 GLY MET ARG VAL TYR HIS VAL HIS SER ASP SER TYR GLU SEQRES 12 A 257 THR GLU ASN GLN HIS TYR GLY ARG SER LEU THR LYS GLU SEQRES 13 A 257 THR ILE LYS ASP GLY VAL SER ARG PHE PHE HIS ASN GLY SEQRES 14 A 257 TYR CYS LEU ARG LYS ASP ALA VAL ALA ALA SER ILE GLN SEQRES 15 A 257 LYS ILE GLU LYS ILE LEU GLN TRP PHE GLU ASN GLN LYS SEQRES 16 A 257 GLN LEU ASN PHE TYR ALA SER SER LEU LEU PHE VAL TYR SEQRES 17 A 257 GLU GLY SER SER GLN GLY GLY SER GLY GLY GLU VAL GLU SEQRES 18 A 257 VAL ARG MET ILE ASP PHE ALA HIS VAL PHE PRO SER ASN SEQRES 19 A 257 THR ILE ASP GLU GLY TYR VAL TYR GLY LEU LYS HIS LEU SEQRES 20 A 257 ILE SER VAL LEU ARG SER ILE LEU ASP ASN HET MG A 701 1 HET MG A 702 1 HET ADP A 703 27 HET I3P A 704 24 HET PO4 A 705 5 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE HETNAM PO4 PHOSPHATE ION FORMUL 2 MG 2(MG 2+) FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 I3P C6 H15 O15 P3 FORMUL 6 PO4 O4 P 3- FORMUL 7 HOH *172(H2 O) HELIX 1 AA1 PRO A 81 TYR A 94 1 14 HELIX 2 AA2 ASP A 100 ARG A 107 1 8 HELIX 3 AA3 LYS A 108 LEU A 110 5 3 HELIX 4 AA4 SER A 157 TYR A 168 1 12 HELIX 5 AA5 LEU A 170 GLY A 175 1 6 HELIX 6 AA6 ASN A 195 SER A 201 1 7 HELIX 7 AA7 THR A 206 ARG A 213 1 8 HELIX 8 AA8 PHE A 214 HIS A 216 5 3 HELIX 9 AA9 ARG A 222 ASN A 242 1 21 HELIX 10 AB1 ASP A 396 LEU A 414 1 19 SHEET 1 AA1 4 LEU A 66 HIS A 68 0 SHEET 2 AA1 4 THR A 72 GLN A 76 -1 O LEU A 74 N LEU A 66 SHEET 3 AA1 4 TYR A 127 GLU A 131 -1 O LEU A 130 N VAL A 73 SHEET 4 AA1 4 TYR A 113 TRP A 117 -1 N TYR A 114 O LYS A 129 SHEET 1 AA2 5 SER A 190 GLU A 194 0 SHEET 2 AA2 5 PHE A 176 HIS A 185 -1 N HIS A 185 O SER A 190 SHEET 3 AA2 5 PRO A 140 ILE A 147 -1 N LYS A 146 O LEU A 177 SHEET 4 AA2 5 SER A 251 GLU A 258 -1 O PHE A 255 N MET A 143 SHEET 5 AA2 5 VAL A 379 ILE A 384 -1 O ARG A 382 N LEU A 254 SHEET 1 AA3 2 LEU A 246 PHE A 248 0 SHEET 2 AA3 2 VAL A 389 PRO A 391 -1 O PHE A 390 N ASN A 247 LINK OD1 ASP A 385 MG MG A 702 1555 1555 2.58 LINK OD2 ASP A 385 MG MG A 702 1555 1555 2.33 LINK OD2 ASP A 385 MG MG A 701 1555 1555 2.18 LINK MG MG A 701 O2A ADP A 703 1555 1555 2.01 LINK MG MG A 701 O HOH A 854 1555 1555 2.16 LINK MG MG A 701 O HOH A 903 1555 1555 2.07 LINK MG MG A 701 O HOH A 925 1555 1555 2.23 LINK MG MG A 701 O3B ADP A 703 1555 1555 1.99 LINK MG MG A 702 O HOH A 859 1555 1555 2.25 LINK MG MG A 702 O1B ADP A 703 1555 1555 2.48 LINK MG MG A 702 O HOH A 803 1555 1555 2.99 LINK MG MG A 702 O HOH A 849 1555 1555 2.08 LINK MG MG A 702 O HOH A 919 1555 1555 1.75 CISPEP 1 PRO A 80 PRO A 81 0 3.60 SITE 1 AC1 5 ASP A 385 ADP A 703 HOH A 854 HOH A 903 SITE 2 AC1 5 HOH A 925 SITE 1 AC2 6 ASP A 385 ADP A 703 HOH A 803 HOH A 849 SITE 2 AC2 6 HOH A 859 HOH A 919 SITE 1 AC3 20 ILE A 65 VAL A 73 LYS A 75 PRO A 111 SITE 2 AC3 20 GLU A 131 ASP A 132 VAL A 133 ASP A 144 SITE 3 AC3 20 LEU A 254 ASP A 385 MG A 701 MG A 702 SITE 4 AC3 20 HOH A 803 HOH A 854 HOH A 884 HOH A 895 SITE 5 AC3 20 HOH A 903 HOH A 908 HOH A 919 HOH A 925 SITE 1 AC4 16 ARG A 82 LYS A 146 LYS A 160 GLN A 163 SITE 2 AC4 16 GLN A 164 LYS A 167 GLN A 196 ALA A 250 SITE 3 AC4 16 HIS A 388 PO4 A 705 HOH A 812 HOH A 819 SITE 4 AC4 16 HOH A 846 HOH A 849 HOH A 871 HOH A 877 SITE 1 AC5 4 LYS A 167 ARG A 200 I3P A 704 HOH A 900 CRYST1 78.015 78.015 85.915 90.00 90.00 90.00 P 42 21 2 8 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 0.012818 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011639 0.00000