data_4IOV # _model_server_result.job_id WNrRjCo2mn2afYBjDKDUNA _model_server_result.datetime_utc '2024-11-15 22:47:01' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4iov # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 4IOV # _exptl.entry_id 4IOV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 70.38 _cell.angle_beta 65.37 _cell.angle_gamma 60.17 _cell.entry_id 4IOV _cell.length_a 246.396 _cell.length_b 247.521 _cell.length_c 250.332 _cell.Z_PDB 61 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IOV _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 60-meric 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 ? 60-meric 60 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B 1 (1-60) A,B 2 1 A,B 3 (1-5) A,B 4 (1,2,6,10,23,24) A,B 5 P A,B 6 (X0)(1-60) # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] P 'transform to point frame' ? ? -0.487905 0.804539 0.338624 0.859902 0.50969 0.02801 -0.150058 0.30485 -0.940505 -0.00006 0.00003 0.00006 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.381746 0.865083 0.325425 -0.628676 0.501127 -0.594675 -0.677522 0.022428 0.73516 -0.00007 0.00002 -0.00001 3 'point symmetry operation' ? ? -0.618609 0.771057 -0.150973 -0.152136 -0.306065 -0.939776 -0.770829 -0.558385 0.306641 -0.00007 0.00008 0.00003 4 'point symmetry operation' ? ? -0.618609 -0.152136 -0.770829 0.771057 -0.306065 -0.558385 -0.150973 -0.939776 0.306641 -0.00001 0.0001 0.00006 5 'point symmetry operation' ? ? 0.381746 -0.628676 -0.677522 0.865083 0.501127 0.022428 0.325425 -0.594675 0.73516 0.00003 0.00005 0.00004 6 'point symmetry operation' ? ? -0.954965 -0.091491 0.282261 -0.091491 -0.814133 -0.573425 0.282261 -0.573425 0.769098 -0.00011 0.00007 0.00004 7 'point symmetry operation' ? ? -0.498275 -0.865642 -0.048855 0.865408 -0.499992 0.032812 -0.05283 -0.02593 0.998267 -0.00005 0.00006 0 8 'point symmetry operation' ? ? 0.387094 -0.865941 0.316708 0.622469 0.498826 0.60308 -0.680214 -0.036308 0.732114 -0.00004 0 -0.00001 9 'point symmetry operation' ? ? 0.477592 -0.091975 0.873754 -0.484575 0.801988 0.349288 -0.732867 -0.590217 0.338454 -0.00009 -0.00005 0.00003 10 'point symmetry operation' ? ? -0.351846 0.386662 0.852465 -0.925826 -0.009465 -0.377832 -0.138024 -0.922173 0.361312 -0.00013 0 0.00006 11 'point symmetry operation' ? ? 0.478863 0.876567 0.048171 0.876567 -0.480432 0.028553 0.048171 0.028553 -0.998431 -0.00004 0.00006 0.00015 12 'point symmetry operation' ? ? -0.40091 0.854608 -0.330024 0.617317 0.518186 0.591948 0.676898 0.033588 -0.73531 -0.00005 0 0.00016 13 'point symmetry operation' ? ? -0.466719 0.074046 -0.881301 -0.491171 0.806984 0.327916 0.735476 0.585913 -0.340265 0 -0.00004 0.00013 14 'point symmetry operation' ? ? 0.372382 -0.38641 -0.843812 -0.917004 -0.013147 -0.398661 0.142953 0.922234 -0.359235 0.00004 0 0.0001 15 'point symmetry operation' ? ? 0.956783 0.109576 -0.269367 -0.071696 -0.808814 -0.583678 -0.281825 0.577766 -0.766004 0.00002 0.00007 0.00011 16 'point symmetry operation' ? ? -0.523898 -0.785077 -0.330433 -0.785077 0.294565 0.544873 -0.330433 0.544873 -0.770667 -0.00003 -0.00007 0.00011 17 'point symmetry operation' ? ? 0.517438 -0.854049 0.053455 -0.854049 -0.519321 -0.030085 0.053455 -0.030085 -0.998117 -0.00001 -0.00001 0.00015 18 'point symmetry operation' ? ? 0.698234 0.020838 0.715566 0.020838 -0.999744 0.00878 0.715566 0.00878 -0.69849 -0.00007 0.00003 0.00016 19 'point symmetry operation' ? ? -0.231364 0.630521 0.740887 0.630521 -0.482776 0.607759 0.740887 0.607759 -0.28586 -0.00012 0 0.00012 20 'point symmetry operation' ? ? -0.986683 0.132439 0.094424 0.132439 0.317152 0.939082 0.094424 0.939082 -0.330468 -0.0001 -0.00006 0.00009 21 'point symmetry operation' ? ? -0.475372 0.466604 0.745857 -0.107267 0.810708 -0.57554 -0.873221 -0.353602 -0.335336 -0.00013 0.00004 0.00007 22 'point symmetry operation' ? ? -0.980149 -0.16068 0.116149 -0.16068 0.300565 -0.940129 0.116149 -0.940129 -0.320416 -0.0001 0.00007 0.00012 23 'point symmetry operation' ? ? -0.351846 -0.925826 -0.138024 0.386662 -0.009465 -0.922173 0.852465 -0.377832 0.361312 -0.00004 0.0001 0.00009 24 'point symmetry operation' ? ? 0.541243 -0.771428 0.334596 0.77835 0.309069 -0.546487 0.318163 0.556215 0.767722 -0.00004 0.00009 0.00002 25 'point symmetry operation' ? ? 0.4649 0.08914 0.880864 0.473085 0.815963 -0.332256 -0.74837 0.57119 0.337171 -0.00009 0.00005 0 26 'point symmetry operation' ? ? 0.6218 -0.764079 0.171896 -0.134188 -0.320181 -0.937805 0.771595 0.56006 -0.301619 -0.00002 0.00008 0.00013 27 'point symmetry operation' ? ? 0.601264 0.158863 0.783099 0.785448 -0.297569 -0.542702 0.14681 0.94139 -0.303696 -0.00008 0.0001 0.00009 28 'point symmetry operation' ? ? -0.40091 0.617317 0.676898 0.854608 0.518186 0.033588 -0.330024 0.591948 -0.73531 -0.00012 0.00004 0.00011 29 'point symmetry operation' ? ? -0.999752 -0.022284 0.00006 -0.022284 0.999737 -0.005348 0.00006 -0.005348 -0.999986 -0.00009 0 0.00015 30 'point symmetry operation' ? ? -0.367682 -0.876034 -0.312049 -0.633394 0.481598 -0.605702 0.680898 -0.025056 -0.73195 -0.00003 0.00002 0.00016 31 'point symmetry operation' ? ? 0.2173 -0.61957 -0.754263 0.631549 -0.49995 0.592618 -0.744262 -0.60513 0.28265 0.00003 0 0.00003 32 'point symmetry operation' ? ? 0.983493 -0.139417 -0.115347 0.153886 0.309095 0.938499 -0.09519 -0.940757 0.325447 0.00001 -0.00005 0.00006 33 'point symmetry operation' ? ? 0.541243 0.77835 0.318163 -0.771428 0.309069 0.556215 0.334596 -0.546487 0.767722 -0.00006 -0.00007 0.00004 34 'point symmetry operation' ? ? -0.498275 0.865408 -0.05283 -0.865642 -0.499992 -0.02593 -0.048855 0.032812 0.998267 -0.00008 -0.00002 0 35 'point symmetry operation' ? ? -0.698482 0.001446 -0.715626 0.001446 -0.999993 -0.003432 -0.715626 -0.003432 0.698475 -0.00002 0.00003 -0.00001 36 'point symmetry operation' ? ? -0.363729 0.917045 -0.16349 -0.390093 0.009423 0.920727 0.845889 0.398671 0.354306 -0.00006 -0.00007 0.00008 37 'point symmetry operation' ? ? -0.604609 0.141234 -0.783901 -0.778654 -0.312091 0.544332 -0.16777 0.939496 0.298665 -0.00002 -0.00006 0.00003 38 'point symmetry operation' ? ? 0.211513 -0.469841 -0.857036 -0.469841 -0.817789 0.33237 -0.857036 0.33237 -0.393724 0.00004 -0.00002 0.00006 39 'point symmetry operation' ? ? 0.956783 -0.071696 -0.281825 0.109576 -0.808814 0.577766 -0.269367 -0.583678 -0.766004 0.00002 -0.00001 0.00013 40 'point symmetry operation' ? ? 0.601264 0.785448 0.14681 0.158863 -0.297569 0.94139 0.783099 -0.542702 -0.303696 -0.00004 -0.00005 0.00014 41 'point symmetry operation' ? ? -0.475372 -0.107267 -0.873221 0.466604 0.810708 -0.353602 0.745857 -0.57554 -0.335336 0 0.00005 0.00014 42 'point symmetry operation' ? ? 0.477592 -0.484575 -0.732867 -0.091975 0.801988 -0.590217 0.873754 0.349288 0.338454 0.00004 0.00004 0.00009 43 'point symmetry operation' ? ? 0.983493 0.153886 -0.09519 -0.139417 0.309095 -0.940757 -0.115347 0.938499 0.325447 0 0.00008 0.00003 44 'point symmetry operation' ? ? 0.343193 0.925784 0.158561 0.389841 0.013189 -0.920788 -0.854542 0.377822 -0.356382 -0.00006 0.0001 0.00006 45 'point symmetry operation' ? ? -0.558434 0.764383 -0.322289 0.764383 0.323203 -0.557906 -0.322289 -0.557906 -0.764769 -0.00006 0.00009 0.00013 46 'point symmetry operation' ? ? 0.2173 0.631549 -0.744262 -0.61957 -0.49995 -0.60513 -0.754263 0.592618 0.28265 0.00001 0.00004 0.00001 47 'point symmetry operation' ? ? 0.190168 0.487777 -0.852003 0.487777 -0.80009 -0.349184 -0.852003 -0.349184 -0.390078 0.00002 0.00008 0.00007 48 'point symmetry operation' ? ? 0.343193 0.389841 -0.854542 0.925784 0.013189 0.377822 0.158561 -0.920788 -0.356382 0.00003 0.00003 0.00012 49 'point symmetry operation' ? ? 0.4649 0.473085 -0.74837 0.08914 0.815963 0.57119 0.880864 -0.332256 0.33717 0.00003 -0.00004 0.0001 50 'point symmetry operation' ? ? 0.387094 0.622469 -0.680214 -0.865941 0.498826 -0.036308 0.316708 0.60308 0.732114 0.00001 -0.00003 0.00003 51 'point symmetry operation' ? ? -0.363729 -0.390093 0.845889 0.917045 0.009423 0.398671 -0.16349 0.920727 0.354306 -0.00012 0.00003 0.00003 52 'point symmetry operation' ? ? -0.466719 -0.491171 0.735476 0.074046 0.806984 0.585913 -0.881301 0.327916 -0.340265 -0.00012 -0.00004 0.00006 53 'point symmetry operation' ? ? -0.367682 -0.633394 0.680898 -0.876034 0.481598 -0.025056 -0.312049 -0.605702 -0.73195 -0.00011 -0.00003 0.00013 54 'point symmetry operation' ? ? -0.203485 -0.620216 0.757579 -0.620216 -0.517062 -0.589898 0.757579 -0.589898 -0.279453 -0.0001 0.00004 0.00014 55 'point symmetry operation' ? ? -0.201042 -0.469848 0.85955 0.487968 -0.808882 -0.32802 0.849394 0.353487 0.39189 -0.00011 0.00007 0.00008 56 'point symmetry operation' ? ? 0.6218 -0.134188 0.771595 -0.764079 -0.320181 0.56006 0.171896 -0.937805 -0.301619 -0.00007 -0.00006 0.00012 57 'point symmetry operation' ? ? -0.201042 0.487968 0.849394 -0.469848 -0.808882 0.353487 0.85955 -0.32802 0.39189 -0.00013 -0.00002 0.00009 58 'point symmetry operation' ? ? -0.959004 0.089667 0.268834 0.089667 -0.803882 0.587991 0.268834 0.587991 0.762886 -0.00011 -0.00001 0.00002 59 'point symmetry operation' ? ? -0.604609 -0.778654 -0.16777 0.141234 -0.312091 0.939496 -0.783901 0.544332 0.298665 -0.00005 -0.00005 0 60 'point symmetry operation' ? ? 0.372382 -0.917004 0.142953 -0.38641 -0.013147 0.922234 -0.843812 -0.398661 -0.359235 -0.00003 -0.00007 0.00007 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O6 P' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O5' C5' D5M sing 83 n n O5' P D5M sing 84 n n C5' C4' D5M sing 85 n n C5' "H5'1" D5M sing 86 n n C5' "H5'2" D5M sing 87 n n C4' O4' D5M sing 88 n n C4' C3' D5M sing 89 n n C4' H4' D5M sing 90 n n O4' C1' D5M sing 91 n n C3' O3' D5M sing 92 n n C3' C2' D5M sing 93 n n C3' H1 D5M sing 94 n n O3' H3' D5M sing 95 n n C2' C1' D5M sing 96 n n C2' "H2'1" D5M sing 97 n n C2' "H2'2" D5M sing 98 n n C1' N9 D5M sing 99 n n C1' H1' D5M sing 100 n n N9 C8 D5M sing 101 n y N9 C4 D5M sing 102 n y C8 N7 D5M doub 103 n y C8 H8 D5M sing 104 n n N7 C5 D5M sing 105 n y C5 C6 D5M sing 106 n y C5 C4 D5M doub 107 n y C6 N6 D5M sing 108 n n C6 N1 D5M doub 109 n y N6 HN61 D5M sing 110 n n N6 HN62 D5M sing 111 n n N1 C2 D5M sing 112 n y C2 N3 D5M doub 113 n y C2 H2 D5M sing 114 n n N3 C4 D5M sing 115 n y P O1P D5M doub 116 n n P O3P D5M sing 117 n n P O2P D5M sing 118 n n O3P H3P D5M sing 119 n n O2P H2P D5M sing 120 n n # _atom_sites.entry_id 4IOV _atom_sites.fract_transf_matrix[1][1] 0.004059 _atom_sites.fract_transf_matrix[1][2] -0.002327 _atom_sites.fract_transf_matrix[1][3] -0.001502 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004657 _atom_sites.fract_transf_matrix[2][3] -0.000769 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004454 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id D5M _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 801 _pdbx_nonpoly_scheme.auth_seq_num 2 _pdbx_nonpoly_scheme.pdb_mon_id D5M _pdbx_nonpoly_scheme.auth_mon_id D5M _pdbx_nonpoly_scheme.pdb_ins_code . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O5' D5M . . . B 2 -27.503 49.942 -76.572 0.7 68.43 ? O5' D5M 801 A 1 HETATM 2 C C5' D5M . . . B 2 -27.718 51.326 -76.815 0.7 61.24 ? C5' D5M 801 A 1 HETATM 3 C C4' D5M . . . B 2 -26.49 52.127 -76.454 0.7 56.74 ? C4' D5M 801 A 1 HETATM 4 O O4' D5M . . . B 2 -25.303 51.628 -77.136 0.7 53 ? O4' D5M 801 A 1 HETATM 5 C C3' D5M . . . B 2 -26.609 53.606 -76.841 0.7 55.36 ? C3' D5M 801 A 1 HETATM 6 O O3' D5M . . . B 2 -26.013 54.397 -75.805 0.7 54.8 ? O3' D5M 801 A 1 HETATM 7 C C2' D5M . . . B 2 -25.717 53.711 -78.065 0.7 53.38 ? C2' D5M 801 A 1 HETATM 8 C C1' D5M . . . B 2 -24.621 52.756 -77.656 0.7 50.38 ? C1' D5M 801 A 1 HETATM 9 N N9 D5M . . . B 2 -23.686 52.336 -78.702 0.7 46.16 ? N9 D5M 801 A 1 HETATM 10 C C8 D5M . . . B 2 -23.92 51.812 -79.95 0.7 44.41 ? C8 D5M 801 A 1 HETATM 11 N N7 D5M . . . B 2 -22.825 51.601 -80.646 0.7 42.82 ? N7 D5M 801 A 1 HETATM 12 C C5 D5M . . . B 2 -21.803 52.005 -79.792 0.7 42.64 ? C5 D5M 801 A 1 HETATM 13 C C6 D5M . . . B 2 -20.4 52.043 -79.932 0.7 41.61 ? C6 D5M 801 A 1 HETATM 14 N N6 D5M . . . B 2 -19.75 51.666 -81.037 0.7 41.44 ? N6 D5M 801 A 1 HETATM 15 N N1 D5M . . . B 2 -19.678 52.491 -78.883 0.7 40.73 ? N1 D5M 801 A 1 HETATM 16 C C2 D5M . . . B 2 -20.323 52.878 -77.778 0.7 40.43 ? C2 D5M 801 A 1 HETATM 17 N N3 D5M . . . B 2 -21.626 52.897 -77.531 0.7 41.86 ? N3 D5M 801 A 1 HETATM 18 C C4 D5M . . . B 2 -22.32 52.444 -78.59 0.7 43.57 ? C4 D5M 801 A 1 HETATM 19 P P D5M . . . B 2 -27.98 48.882 -77.662 0.7 72.86 ? P D5M 801 A 1 HETATM 20 O O1P D5M . . . B 2 -29.476 48.942 -77.747 0.7 73.55 ? O1P D5M 801 A 1 HETATM 21 O O3P D5M . . . B 2 -27.543 47.632 -77.002 0.7 73.31 ? O3P D5M 801 A 1 HETATM 22 O O2P D5M . . . B 2 -27.158 49.14 -78.892 0.7 73.23 ? O2P D5M 801 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 22 #