HEADER HYDROLASE 30-APR-15 4ZKL TITLE CRYSTAL STRUCTURE OF HUMAN HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN TITLE 2 1 (HHINT1) COMPLEXED WITH JB419 (AP4A ANALOG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 1-126; COMPND 5 SYNONYM: ADENOSINE 5'-MONOPHOSPHORAMIDASE,PROTEIN KINASE C INHIBITOR COMPND 6 1,PROTEIN KINASE C-INTERACTING PROTEIN 1,PKCI-1; COMPND 7 EC: 3.-.-.-; 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: HINT1, HINT, PKCI1, PRKCNH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSGA02 KEYWDS HINT, HIT, HYDROLASE, PHOSPHORAMIDASE, COMPLEX, AP4A ANALOG EXPDTA X-RAY DIFFRACTION AUTHOR R.M.DOLOT,R.KACZMAREK,A.SEDA,A.KRAKOWIAK,J.BARANIAK,B.NAWROT REVDAT 4 10-JAN-24 4ZKL 1 REMARK REVDAT 3 07-MAR-18 4ZKL 1 REMARK REVDAT 2 09-MAR-16 4ZKL 1 JRNL REVDAT 1 02-MAR-16 4ZKL 0 JRNL AUTH R.DOLOT,R.KACZMAREK,A.SEDA,A.KRAKOWIAK,J.BARANIAK,B.NAWROT JRNL TITL CRYSTALLOGRAPHIC STUDIES OF THE COMPLEX OF HUMAN HINT1 JRNL TITL 2 PROTEIN WITH A NON-HYDROLYZABLE ANALOG OF AP4A. JRNL REF INT.J.BIOL.MACROMOL. V. 87 62 2016 JRNL REFN ISSN 0141-8130 JRNL PMID 26905466 JRNL DOI 10.1016/J.IJBIOMAC.2016.02.047 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 102.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 23826 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1222 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) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1774 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3495 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.12000 REMARK 3 B22 (A**2) : -4.22000 REMARK 3 B33 (A**2) : 1.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.297 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.229 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.237 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.980 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3705 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3537 ; 0.013 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5018 ; 2.162 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8176 ; 1.917 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 451 ; 6.899 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;38.924 ;24.013 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 624 ;17.120 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.623 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 540 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4095 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 830 ; 0.010 ; 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): 1810 ; 2.392 ; 2.654 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1809 ; 2.392 ; 2.653 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2259 ; 4.088 ; 3.963 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2260 ; 4.087 ; 3.964 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1895 ; 2.567 ; 3.025 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1895 ; 2.567 ; 3.025 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2760 ; 4.330 ; 4.460 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4133 ; 9.234 ;22.508 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4134 ; 9.233 ;22.520 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 15 125 B 15 125 12798 0.08 0.05 REMARK 3 2 A 15 126 C 15 126 13128 0.07 0.05 REMARK 3 3 A 15 125 D 15 125 12628 0.10 0.05 REMARK 3 4 B 15 125 C 15 125 12800 0.08 0.05 REMARK 3 5 B 14 125 D 14 125 12724 0.11 0.05 REMARK 3 6 C 15 125 D 15 125 12718 0.09 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 17 A 126 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5302 -0.6724 4.1943 REMARK 3 T TENSOR REMARK 3 T11: 0.1131 T22: 0.2254 REMARK 3 T33: 0.7300 T12: -0.0057 REMARK 3 T13: 0.0514 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 2.5177 L22: 2.5803 REMARK 3 L33: 0.4080 L12: -0.1553 REMARK 3 L13: 0.4218 L23: 0.0167 REMARK 3 S TENSOR REMARK 3 S11: 0.0458 S12: -0.0197 S13: 0.1360 REMARK 3 S21: 0.3373 S22: -0.0572 S23: 0.0710 REMARK 3 S31: 0.0013 S32: 0.0535 S33: 0.0114 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 17 B 126 REMARK 3 ORIGIN FOR THE GROUP (A): 23.8975 -1.2305 6.1359 REMARK 3 T TENSOR REMARK 3 T11: 0.0833 T22: 0.2131 REMARK 3 T33: 0.7276 T12: -0.0002 REMARK 3 T13: -0.0062 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 2.5797 L22: 2.8175 REMARK 3 L33: 0.9703 L12: 0.7650 REMARK 3 L13: -0.0386 L23: -0.1711 REMARK 3 S TENSOR REMARK 3 S11: 0.1382 S12: 0.0075 S13: 0.0062 REMARK 3 S21: 0.2403 S22: -0.0645 S23: -0.2741 REMARK 3 S31: 0.0285 S32: 0.0361 S33: -0.0737 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 17 C 126 REMARK 3 ORIGIN FOR THE GROUP (A): 25.4825 -12.4843 44.3633 REMARK 3 T TENSOR REMARK 3 T11: 0.7197 T22: 0.0115 REMARK 3 T33: 0.3682 T12: -0.0237 REMARK 3 T13: 0.0078 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 1.3724 L22: 1.9582 REMARK 3 L33: 3.4605 L12: -0.1365 REMARK 3 L13: -0.7317 L23: -1.3264 REMARK 3 S TENSOR REMARK 3 S11: -0.0750 S12: 0.1124 S13: -0.0302 REMARK 3 S21: 0.1057 S22: -0.0083 S23: -0.0002 REMARK 3 S31: 0.1658 S32: -0.0656 S33: 0.0833 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 17 D 126 REMARK 3 ORIGIN FOR THE GROUP (A): 35.5449 -11.8571 28.8197 REMARK 3 T TENSOR REMARK 3 T11: 0.5182 T22: 0.0739 REMARK 3 T33: 0.3015 T12: 0.0529 REMARK 3 T13: -0.0146 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 2.3748 L22: 2.4600 REMARK 3 L33: 3.7522 L12: -0.4197 REMARK 3 L13: -0.0315 L23: 0.5123 REMARK 3 S TENSOR REMARK 3 S11: 0.1731 S12: 0.1649 S13: -0.0984 REMARK 3 S21: 0.0800 S22: -0.1039 S23: -0.2675 REMARK 3 S31: 0.1630 S32: 0.4410 S33: -0.0692 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 4ZKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96690 REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 REMARK 200 RESOLUTION RANGE LOW (A) : 102.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.69200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3TW2 REMARK 200 REMARK 200 REMARK: PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% W/V PEG4000, 0.1 M SODIUM REMARK 280 CACODYLATE PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.20950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 4360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 ALA A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 4 REMARK 465 ILE A 5 REMARK 465 ALA A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 GLN A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 ARG A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 3 REMARK 465 GLU B 4 REMARK 465 ILE B 5 REMARK 465 ALA B 6 REMARK 465 LYS B 7 REMARK 465 ALA B 8 REMARK 465 GLN B 9 REMARK 465 VAL B 10 REMARK 465 ALA B 11 REMARK 465 ARG B 12 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 ASP C 3 REMARK 465 GLU C 4 REMARK 465 ILE C 5 REMARK 465 ALA C 6 REMARK 465 LYS C 7 REMARK 465 ALA C 8 REMARK 465 GLN C 9 REMARK 465 VAL C 10 REMARK 465 ALA C 11 REMARK 465 ARG C 12 REMARK 465 PRO C 13 REMARK 465 GLY C 14 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 ASP D 3 REMARK 465 GLU D 4 REMARK 465 ILE D 5 REMARK 465 ALA D 6 REMARK 465 LYS D 7 REMARK 465 ALA D 8 REMARK 465 GLN D 9 REMARK 465 VAL D 10 REMARK 465 ALA D 11 REMARK 465 ARG D 12 REMARK 465 PRO D 13 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 OD1 ASP B 43 O35 JB6 B 202 1.90 REMARK 500 O34 JB6 B 202 O HOH B 301 2.17 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 34 CD GLU A 34 OE1 0.074 REMARK 500 GLU A 71 CD GLU A 71 OE1 0.085 REMARK 500 GLU B 71 CG GLU B 71 CD 0.111 REMARK 500 GLU B 71 CD GLU B 71 OE1 0.069 REMARK 500 ASP C 69 CB ASP C 69 CG 0.131 REMARK 500 SER D 64 CB SER D 64 OG -0.083 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 A 35 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 35 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP B 35 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 35 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP B 36 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 69 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP C 35 CB - CG - OD1 ANGL. DEV. = 9.1 DEGREES REMARK 500 ASP C 35 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP D 35 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP D 35 CB - CG - OD2 ANGL. DEV. = -5.7 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 ARG A 24 1.65 -68.66 REMARK 500 SER A 45 78.14 -117.63 REMARK 500 ASP B 16 44.07 -87.13 REMARK 500 SER C 45 75.54 -117.11 REMARK 500 SER C 45 75.92 -115.35 REMARK 500 ASP D 16 40.86 -88.05 REMARK 500 SER D 45 72.74 -118.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP B 35 11.44 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 275 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 276 DISTANCE = 7.85 ANGSTROMS REMARK 525 HOH B 365 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B 366 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH B 367 DISTANCE = 7.50 ANGSTROMS REMARK 525 HOH B 368 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH C 231 DISTANCE = 5.85 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JB6 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TW2 RELATED DB: PDB REMARK 900 3TW2 CONTAINS THE SAME PROTEIN WITH AMP REMARK 900 RELATED ID: 1KPC RELATED DB: PDB REMARK 900 1KPC WAS CRYSTALLIZED IN THE SAME SPACE GROUP WITHOUT LIGAND DBREF 4ZKL A 1 126 UNP P49773 HINT1_HUMAN 1 126 DBREF 4ZKL B 1 126 UNP P49773 HINT1_HUMAN 1 126 DBREF 4ZKL C 1 126 UNP P49773 HINT1_HUMAN 1 126 DBREF 4ZKL D 1 126 UNP P49773 HINT1_HUMAN 1 126 SEQRES 1 A 126 MET ALA ASP GLU ILE ALA LYS ALA GLN VAL ALA ARG PRO SEQRES 2 A 126 GLY GLY ASP THR ILE PHE GLY LYS ILE ILE ARG LYS GLU SEQRES 3 A 126 ILE PRO ALA LYS ILE ILE PHE GLU ASP ASP ARG CYS LEU SEQRES 4 A 126 ALA PHE HIS ASP ILE SER PRO GLN ALA PRO THR HIS PHE SEQRES 5 A 126 LEU VAL ILE PRO LYS LYS HIS ILE SER GLN ILE SER VAL SEQRES 6 A 126 ALA GLU ASP ASP ASP GLU SER LEU LEU GLY HIS LEU MET SEQRES 7 A 126 ILE VAL GLY LYS LYS CYS ALA ALA ASP LEU GLY LEU ASN SEQRES 8 A 126 LYS GLY TYR ARG MET VAL VAL ASN GLU GLY SER ASP GLY SEQRES 9 A 126 GLY GLN SER VAL TYR HIS VAL HIS LEU HIS VAL LEU GLY SEQRES 10 A 126 GLY ARG GLN MET HIS TRP PRO PRO GLY SEQRES 1 B 126 MET ALA ASP GLU ILE ALA LYS ALA GLN VAL ALA ARG PRO SEQRES 2 B 126 GLY GLY ASP THR ILE PHE GLY LYS ILE ILE ARG LYS GLU SEQRES 3 B 126 ILE PRO ALA LYS ILE ILE PHE GLU ASP ASP ARG CYS LEU SEQRES 4 B 126 ALA PHE HIS ASP ILE SER PRO GLN ALA PRO THR HIS PHE SEQRES 5 B 126 LEU VAL ILE PRO LYS LYS HIS ILE SER GLN ILE SER VAL SEQRES 6 B 126 ALA GLU ASP ASP ASP GLU SER LEU LEU GLY HIS LEU MET SEQRES 7 B 126 ILE VAL GLY LYS LYS CYS ALA ALA ASP LEU GLY LEU ASN SEQRES 8 B 126 LYS GLY TYR ARG MET VAL VAL ASN GLU GLY SER ASP GLY SEQRES 9 B 126 GLY GLN SER VAL TYR HIS VAL HIS LEU HIS VAL LEU GLY SEQRES 10 B 126 GLY ARG GLN MET HIS TRP PRO PRO GLY SEQRES 1 C 126 MET ALA ASP GLU ILE ALA LYS ALA GLN VAL ALA ARG PRO SEQRES 2 C 126 GLY GLY ASP THR ILE PHE GLY LYS ILE ILE ARG LYS GLU SEQRES 3 C 126 ILE PRO ALA LYS ILE ILE PHE GLU ASP ASP ARG CYS LEU SEQRES 4 C 126 ALA PHE HIS ASP ILE SER PRO GLN ALA PRO THR HIS PHE SEQRES 5 C 126 LEU VAL ILE PRO LYS LYS HIS ILE SER GLN ILE SER VAL SEQRES 6 C 126 ALA GLU ASP ASP ASP GLU SER LEU LEU GLY HIS LEU MET SEQRES 7 C 126 ILE VAL GLY LYS LYS CYS ALA ALA ASP LEU GLY LEU ASN SEQRES 8 C 126 LYS GLY TYR ARG MET VAL VAL ASN GLU GLY SER ASP GLY SEQRES 9 C 126 GLY GLN SER VAL TYR HIS VAL HIS LEU HIS VAL LEU GLY SEQRES 10 C 126 GLY ARG GLN MET HIS TRP PRO PRO GLY SEQRES 1 D 126 MET ALA ASP GLU ILE ALA LYS ALA GLN VAL ALA ARG PRO SEQRES 2 D 126 GLY GLY ASP THR ILE PHE GLY LYS ILE ILE ARG LYS GLU SEQRES 3 D 126 ILE PRO ALA LYS ILE ILE PHE GLU ASP ASP ARG CYS LEU SEQRES 4 D 126 ALA PHE HIS ASP ILE SER PRO GLN ALA PRO THR HIS PHE SEQRES 5 D 126 LEU VAL ILE PRO LYS LYS HIS ILE SER GLN ILE SER VAL SEQRES 6 D 126 ALA GLU ASP ASP ASP GLU SER LEU LEU GLY HIS LEU MET SEQRES 7 D 126 ILE VAL GLY LYS LYS CYS ALA ALA ASP LEU GLY LEU ASN SEQRES 8 D 126 LYS GLY TYR ARG MET VAL VAL ASN GLU GLY SER ASP GLY SEQRES 9 D 126 GLY GLN SER VAL TYR HIS VAL HIS LEU HIS VAL LEU GLY SEQRES 10 D 126 GLY ARG GLN MET HIS TRP PRO PRO GLY HET AMP B 201 23 HET JB6 B 202 51 HET AMP D 201 23 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM JB6 (2R,3R,4S,5R)-2-(6-AMINOPURIN-9-YL)-5-[2-[[(2S)-3- HETNAM 2 JB6 [[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4- HETNAM 3 JB6 BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-SULFANYL- HETNAM 4 JB6 PHOSPHORYL]OXY-2-OXIDANYL-PROPOXY]-SULFANYL- HETNAM 5 JB6 PHOSPHORYL]OXYETHYL]OXOLANE-3,4-DIOL FORMUL 5 AMP 2(C10 H14 N5 O7 P) FORMUL 6 JB6 C24 H34 N10 O13 P2 S2 FORMUL 8 HOH *194(H2 O) HELIX 1 AA1 THR A 17 ARG A 24 1 8 HELIX 2 AA2 GLN A 62 ALA A 66 5 5 HELIX 3 AA3 GLU A 67 ASP A 69 5 3 HELIX 4 AA4 ASP A 70 LEU A 88 1 19 HELIX 5 AA5 GLY A 101 GLY A 105 1 5 HELIX 6 AA6 THR B 17 ARG B 24 1 8 HELIX 7 AA7 GLN B 62 ALA B 66 5 5 HELIX 8 AA8 GLU B 67 ASP B 69 5 3 HELIX 9 AA9 ASP B 70 LEU B 88 1 19 HELIX 10 AB1 GLY B 101 GLY B 105 1 5 HELIX 11 AB2 THR C 17 ARG C 24 1 8 HELIX 12 AB3 GLN C 62 ALA C 66 5 5 HELIX 13 AB4 GLU C 67 ASP C 69 5 3 HELIX 14 AB5 ASP C 70 LEU C 88 1 19 HELIX 15 AB6 GLY C 101 GLY C 105 1 5 HELIX 16 AB7 THR D 17 ARG D 24 1 8 HELIX 17 AB8 GLN D 62 ALA D 66 5 5 HELIX 18 AB9 GLU D 67 ASP D 69 5 3 HELIX 19 AC1 ASP D 70 LEU D 88 1 19 HELIX 20 AC2 GLY D 101 GLY D 105 1 5 SHEET 1 AA110 ILE A 31 GLU A 34 0 SHEET 2 AA110 CYS A 38 HIS A 42 -1 O ALA A 40 N ILE A 32 SHEET 3 AA110 THR A 50 PRO A 56 -1 O LEU A 53 N PHE A 41 SHEET 4 AA110 LEU A 113 GLY A 117 -1 O VAL A 115 N PHE A 52 SHEET 5 AA110 TYR A 94 GLU A 100 -1 N VAL A 97 O HIS A 114 SHEET 6 AA110 TYR B 94 GLU B 100 -1 O MET B 96 N VAL A 98 SHEET 7 AA110 LEU B 113 GLY B 117 -1 O HIS B 114 N VAL B 97 SHEET 8 AA110 THR B 50 PRO B 56 -1 N PHE B 52 O VAL B 115 SHEET 9 AA110 CYS B 38 HIS B 42 -1 N PHE B 41 O LEU B 53 SHEET 10 AA110 ILE B 31 GLU B 34 -1 N ILE B 32 O ALA B 40 SHEET 1 AA210 ILE C 31 GLU C 34 0 SHEET 2 AA210 CYS C 38 HIS C 42 -1 O ALA C 40 N ILE C 32 SHEET 3 AA210 THR C 50 PRO C 56 -1 O LEU C 53 N PHE C 41 SHEET 4 AA210 LEU C 113 GLY C 117 -1 O VAL C 115 N PHE C 52 SHEET 5 AA210 TYR C 94 GLU C 100 -1 N VAL C 97 O HIS C 114 SHEET 6 AA210 TYR D 94 GLU D 100 -1 O MET D 96 N VAL C 98 SHEET 7 AA210 LEU D 113 GLY D 117 -1 O HIS D 114 N VAL D 97 SHEET 8 AA210 THR D 50 PRO D 56 -1 N PHE D 52 O VAL D 115 SHEET 9 AA210 CYS D 38 HIS D 42 -1 N PHE D 41 O LEU D 53 SHEET 10 AA210 ILE D 31 GLU D 34 -1 N ILE D 32 O ALA D 40 CISPEP 1 TRP A 123 PRO A 124 0 5.68 CISPEP 2 TRP B 123 PRO B 124 0 8.89 CISPEP 3 TRP C 123 PRO C 124 0 6.88 CISPEP 4 TRP D 123 PRO D 124 0 5.84 SITE 1 AC1 14 PHE B 19 PHE B 41 HIS B 42 ASP B 43 SITE 2 AC1 14 ILE B 44 ASN B 99 GLY B 105 GLN B 106 SITE 3 AC1 14 SER B 107 HIS B 112 HIS B 114 JB6 B 202 SITE 4 AC1 14 HOH B 301 HOH B 304 SITE 1 AC2 27 ILE B 22 PHE B 41 HIS B 42 ASP B 43 SITE 2 AC2 27 ILE B 44 SER B 45 GLY B 105 SER B 107 SITE 3 AC2 27 VAL B 108 HIS B 112 AMP B 201 HOH B 301 SITE 4 AC2 27 HOH B 304 HOH B 332 PHE D 19 HIS D 42 SITE 5 AC2 27 ASP D 43 ILE D 44 SER D 45 LEU D 53 SITE 6 AC2 27 GLY D 105 SER D 107 VAL D 108 HIS D 112 SITE 7 AC2 27 HIS D 114 AMP D 201 HOH D 305 SITE 1 AC3 15 JB6 B 202 HOH B 332 PHE D 19 HIS D 42 SITE 2 AC3 15 ASP D 43 ILE D 44 SER D 45 ASN D 99 SITE 3 AC3 15 GLY D 105 GLN D 106 SER D 107 VAL D 108 SITE 4 AC3 15 HIS D 112 HIS D 114 HOH D 305 CRYST1 63.714 46.419 103.413 90.00 97.41 90.00 P 1 21 1 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 0.015695 0.000000 0.002040 0.00000 SCALE2 0.000000 0.021543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009751 0.00000