HEADER HYDROLASE 22-MAR-18 6G22 TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUCLEOTIDASE TITLE 2 IN COMPLEX WITH THE INHIBITOR PB-PEU COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'(3')-DEOXYRIBONUCLEOTIDASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5',3'-NUCLEOTIDASE,MITOCHONDRIAL,DEOXY-5'-NUCLEOTIDASE 2, COMPND 5 DNT-2; COMPND 6 EC: 3.1.3.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NT5M, DNT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS 5'-NUCLEOTIDASE, DEPHOSPHORYLATION, PHOSPHORYLATION, HAD-LIKE, KEYWDS 2 MITOCHONDRIA, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,P.REZACOVA,J.BRYNDA REVDAT 3 17-JAN-24 6G22 1 LINK REVDAT 2 06-FEB-19 6G22 1 JRNL REVDAT 1 11-JUL-18 6G22 0 JRNL AUTH P.PACHL,O.SIMAK,M.BUDESINSKY,J.BRYNDA,I.ROSENBERG,P.REZACOVA JRNL TITL STRUCTURE-BASED OPTIMIZATION OF BISPHOSPHONATE NUCLEOSIDE JRNL TITL 2 INHIBITORS OF HUMAN 5'(3')-DEOXYRIBONUCLEOTIDASES JRNL REF EUR.J.ORG.CHEM. 2018 JRNL REFN ISSN 1434-193X JRNL DOI 10.1002/EJOC.201800515 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 24012 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1264 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1743 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1583 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : 0.55000 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): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.467 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1713 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1567 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2334 ; 1.794 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3640 ; 0.982 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 202 ; 5.703 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;29.624 ;23.253 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 280 ;12.918 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;15.421 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 245 ; 0.161 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1863 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 378 ; 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): 781 ; 2.349 ; 2.471 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 780 ; 2.340 ; 2.466 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 977 ; 3.297 ; 3.684 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 978 ; 3.297 ; 3.689 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 932 ; 3.131 ; 2.810 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 933 ; 3.130 ; 2.810 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1353 ; 4.724 ; 4.079 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2076 ; 6.338 ;30.298 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2013 ; 6.142 ;29.509 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6G22 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47028 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 43.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.350 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.77 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.460 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: 4YIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 8% PEG8000, 10% GYCEROL, PH 4, PH 8, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 53.28150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.87650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.87650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.92225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.87650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.87650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.64075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.87650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.87650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.92225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.87650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.87650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.64075 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 53.28150 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: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.28150 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 585 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 629 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 SER A 27 REMARK 465 ASN A 28 REMARK 465 ALA A 29 REMARK 465 ALA A 30 REMARK 465 SER A 31 REMARK 465 GLY A 32 REMARK 465 GLY A 33 REMARK 465 ARG A 34 REMARK 465 CYS A 228 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 55 NE CZ NH1 NH2 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 MET A 42 -67.63 -98.04 REMARK 500 VAL A 45 -53.95 -128.13 REMARK 500 ASN A 100 -3.08 72.21 REMARK 500 PRO A 207 36.03 -97.04 REMARK 500 SER A 213 173.75 178.27 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 41 OD2 REMARK 620 2 ASP A 43 O 86.7 REMARK 620 3 ASP A 176 OD1 84.7 89.2 REMARK 620 4 2O2 A 305 OBG 105.4 98.4 167.5 REMARK 620 5 HOH A 437 O 168.0 88.7 84.1 86.3 REMARK 620 6 HOH A 444 O 85.6 171.9 87.7 86.0 98.5 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2O2 A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6G2L RELATED DB: PDB REMARK 900 RELATED ID: 6G2M RELATED DB: PDB REMARK 900 RELATED ID: 6G2N RELATED DB: PDB DBREF 6G22 A 32 228 UNP Q9NPB1 NT5M_HUMAN 32 228 SEQADV 6G22 SER A 27 UNP Q9NPB1 EXPRESSION TAG SEQADV 6G22 ASN A 28 UNP Q9NPB1 EXPRESSION TAG SEQADV 6G22 ALA A 29 UNP Q9NPB1 EXPRESSION TAG SEQADV 6G22 ALA A 30 UNP Q9NPB1 EXPRESSION TAG SEQADV 6G22 SER A 31 UNP Q9NPB1 EXPRESSION TAG SEQRES 1 A 202 SER ASN ALA ALA SER GLY GLY ARG ALA LEU ARG VAL LEU SEQRES 2 A 202 VAL ASP MET ASP GLY VAL LEU ALA ASP PHE GLU GLY GLY SEQRES 3 A 202 PHE LEU ARG LYS PHE ARG ALA ARG PHE PRO ASP GLN PRO SEQRES 4 A 202 PHE ILE ALA LEU GLU ASP ARG ARG GLY PHE TRP VAL SER SEQRES 5 A 202 GLU GLN TYR GLY ARG LEU ARG PRO GLY LEU SER GLU LYS SEQRES 6 A 202 ALA ILE SER ILE TRP GLU SER LYS ASN PHE PHE PHE GLU SEQRES 7 A 202 LEU GLU PRO LEU PRO GLY ALA VAL GLU ALA VAL LYS GLU SEQRES 8 A 202 MET ALA SER LEU GLN ASN THR ASP VAL PHE ILE CYS THR SEQRES 9 A 202 SER PRO ILE LYS MET PHE LYS TYR CYS PRO TYR GLU LYS SEQRES 10 A 202 TYR ALA TRP VAL GLU LYS TYR PHE GLY PRO ASP PHE LEU SEQRES 11 A 202 GLU GLN ILE VAL LEU THR ARG ASP LYS THR VAL VAL SER SEQRES 12 A 202 ALA ASP LEU LEU ILE ASP ASP ARG PRO ASP ILE THR GLY SEQRES 13 A 202 ALA GLU PRO THR PRO SER TRP GLU HIS VAL LEU PHE THR SEQRES 14 A 202 ALA CYS HIS ASN GLN HIS LEU GLN LEU GLN PRO PRO ARG SEQRES 15 A 202 ARG ARG LEU HIS SER TRP ALA ASP ASP TRP LYS ALA ILE SEQRES 16 A 202 LEU ASP SER LYS ARG PRO CYS HET MG A 301 1 HET BME A 302 4 HET GOL A 303 6 HET GOL A 304 6 HET 2O2 A 305 33 HETNAM MG MAGNESIUM ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM GOL GLYCEROL HETNAM 2O2 1-{2-DEOXY-3,5-O-[PHENYL(PHOSPHONO)METHYLIDENE]-BETA-D- HETNAM 2 2O2 THREO-PENTOFURANOSYL}-5-[(E)-2- HETNAM 3 2O2 PHOSPHONOETHENYL]PYRIMIDINE-2,4(1H,3H)-DIONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 BME C2 H6 O S FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 2O2 C18 H20 N2 O11 P2 FORMUL 7 HOH *236(H2 O) HELIX 1 AA1 ASP A 48 PHE A 61 1 14 HELIX 2 AA2 ALA A 68 ARG A 72 5 5 HELIX 3 AA3 TRP A 76 ARG A 85 1 10 HELIX 4 AA4 GLY A 87 GLU A 97 1 11 HELIX 5 AA5 GLY A 110 LEU A 121 1 12 HELIX 6 AA6 TYR A 138 GLY A 152 1 15 HELIX 7 AA7 PRO A 153 GLU A 157 5 5 HELIX 8 AA8 ALA A 196 GLN A 200 5 5 HELIX 9 AA9 ASP A 217 SER A 224 1 8 SHEET 1 AA1 6 ILE A 159 LEU A 161 0 SHEET 2 AA1 6 THR A 124 THR A 130 1 N ILE A 128 O VAL A 160 SHEET 3 AA1 6 LEU A 36 VAL A 40 1 N VAL A 38 O ASP A 125 SHEET 4 AA1 6 LEU A 172 ASP A 175 1 O LEU A 172 N LEU A 39 SHEET 5 AA1 6 GLU A 190 PHE A 194 1 O VAL A 192 N LEU A 173 SHEET 6 AA1 6 ARG A 209 LEU A 211 1 O LEU A 211 N LEU A 193 LINK SG CYS A 197 S2 BME A 302 1555 1555 2.05 LINK OD2 ASP A 41 MG MG A 301 1555 1555 2.02 LINK O ASP A 43 MG MG A 301 1555 1555 2.09 LINK OD1 ASP A 176 MG MG A 301 1555 1555 2.20 LINK MG MG A 301 OBG 2O2 A 305 1555 1555 2.09 LINK MG MG A 301 O HOH A 437 1555 1555 1.96 LINK MG MG A 301 O HOH A 444 1555 1555 2.09 CISPEP 1 PRO A 206 PRO A 207 0 2.05 SITE 1 AC1 6 ASP A 41 ASP A 43 ASP A 176 2O2 A 305 SITE 2 AC1 6 HOH A 437 HOH A 444 SITE 1 AC2 2 CYS A 197 GLN A 200 SITE 1 AC3 6 TRP A 76 ARG A 177 PRO A 178 ASP A 179 SITE 2 AC3 6 HOH A 462 HOH A 609 SITE 1 AC4 8 ALA A 119 SER A 120 LEU A 121 ASN A 123 SITE 2 AC4 8 THR A 124 HOH A 438 HOH A 478 HOH A 523 SITE 1 AC5 23 ASP A 41 ASP A 43 PHE A 49 PHE A 75 SITE 2 AC5 23 TRP A 76 VAL A 77 TRP A 96 SER A 131 SITE 3 AC5 23 ILE A 133 LYS A 134 ARG A 163 MG A 301 SITE 4 AC5 23 HOH A 402 HOH A 413 HOH A 420 HOH A 422 SITE 5 AC5 23 HOH A 429 HOH A 437 HOH A 441 HOH A 444 SITE 6 AC5 23 HOH A 500 HOH A 506 HOH A 534 CRYST1 73.753 73.753 106.563 90.00 90.00 90.00 P 43 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 0.013559 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013559 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009384 0.00000