data_6L3G # _model_server_result.job_id vshMj6OvmvfpGT9w5U2Hbw _model_server_result.datetime_utc '2024-11-30 03:34:44' _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 6l3g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6L3G # _exptl.entry_id 6L3G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 6L3G _cell.length_a 131.265 _cell.length_b 131.265 _cell.length_c 117.183 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6L3G _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 -y,-x,-z+2/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 78.122 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 B OG1 THR 35 A THR 35 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc2 D O1B ADP . A ADP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc3 D O3B ADP . A ADP 501 1_555 F AL ALF . A ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc4 E MG MG . A MG 502 1_555 F F3 ALF . A ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc5 E MG MG . A MG 502 1_555 J O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc6 C OG1 THR 35 B THR 35 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc7 G O3B ADP . B ADP 501 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc8 G O2B ADP . B ADP 501 1_555 I AL ALF . B ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc9 H MG MG . B MG 502 1_555 I F3 ALF . B ALF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc10 H MG MG . B MG 502 1_555 K O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? hydrog WATSON-CRICK hydrog1 A N1 DG 12 D DG 12 1_555 A N3 DC 19 D DC 19 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 12 D DG 12 1_555 A O2 DC 19 D DC 19 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 12 D DG 12 1_555 A N4 DC 19 D DC 19 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DC 13 D DC 13 1_555 A N1 DG 18 D DG 18 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 DC 13 D DC 13 1_555 A O6 DG 18 D DG 18 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 DC 13 D DC 13 1_555 A N2 DG 18 D DG 18 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DG 14 D DG 14 1_555 A N3 DC 17 D DC 17 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 DG 14 D DG 14 1_555 A O2 DC 17 D DC 17 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 DG 14 D DG 14 1_555 A N4 DC 17 D DC 17 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 DC 15 D DC 15 1_555 A N1 DG 16 D DG 16 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N4 DC 15 D DC 15 1_555 A O6 DG 16 D DG 16 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O2 DC 15 D DC 15 1_555 A N2 DG 16 D DG 16 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DG 16 D DG 16 1_555 A N3 DC 15 D DC 15 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N2 DG 16 D DG 16 1_555 A O2 DC 15 D DC 15 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 DG 16 D DG 16 1_555 A N4 DC 15 D DC 15 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 17 D DC 17 1_555 A N1 DG 14 D DG 14 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 17 D DC 17 1_555 A O6 DG 14 D DG 14 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 17 D DC 17 1_555 A N2 DG 14 D DG 14 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 DG 18 D DG 18 1_555 A N3 DC 13 D DC 13 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 DG 18 D DG 18 1_555 A O2 DC 13 D DC 13 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 DG 18 D DG 18 1_555 A N4 DC 13 D DC 13 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 DC 19 D DC 19 1_555 A N1 DG 12 D DG 12 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 DC 19 D DC 19 1_555 A O6 DG 12 D DG 12 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 DC 19 D DC 19 1_555 A N2 DG 12 D DG 12 4_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6L3G _atom_sites.fract_transf_matrix[1][1] 0.007618 _atom_sites.fract_transf_matrix[1][2] 0.004398 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008797 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008534 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 3 ADP A 1 501 501 ADP ADP . E 4 MG A 1 502 502 MG MG . F 5 ALF A 1 503 503 ALF ALF . G 3 ADP B 1 501 501 ADP ADP . H 4 MG B 1 502 502 MG MG . I 5 ALF B 1 503 503 ALF ALF . J 6 HOH A 1 601 2 HOH HOH . J 6 HOH A 2 602 1 HOH HOH . K 6 HOH B 1 601 5 HOH HOH . K 6 HOH B 2 602 4 HOH HOH . K 6 HOH B 3 603 3 HOH HOH . # 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 P PB ADP . . . D 3 -1.141 -56.01 56.819 1 60.58 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . D 3 -0.23 -55.097 56.036 1 52.78 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . D 3 -0.639 -57.422 56.968 1 64.64 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . D 3 -2.594 -55.916 56.42 1 68.82 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . D 3 0.286 -55.147 59.079 1 63.36 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . D 3 1.384 -55.792 58.271 1 56.23 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . D 3 0.314 -53.661 59.356 1 79.1 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . D 3 -1.108 -55.427 58.322 1 72.01 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . D 3 0.167 -55.889 60.504 1 65.24 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . D 3 -0.951 -56.708 60.822 1 71.63 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . D 3 -1.012 -56.921 62.331 1 73.62 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . D 3 -1.068 -58.324 62.602 1 80.71 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . D 3 0.208 -56.38 63.06 1 70.44 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . D 3 -0.086 -55.133 63.693 1 76.57 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . D 3 0.532 -57.432 64.097 1 63.13 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . D 3 -0.114 -57.096 65.325 1 68.3 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . D 3 -0.079 -58.709 63.558 1 73.9 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . D 3 0.979 -59.461 62.844 1 80.25 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . D 3 1.306 -59.299 61.546 1 69.08 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . D 3 2.314 -60.127 61.181 1 70.19 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . D 3 2.649 -60.846 62.266 1 76.54 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . D 3 3.636 -61.904 62.572 1 78.97 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . D 3 4.483 -62.365 61.623 1 88.07 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . D 3 3.665 -62.392 63.83 1 88.9 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . D 3 2.828 -61.941 64.782 1 93.97 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . D 3 1.906 -60.983 64.576 1 85.63 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . D 3 1.769 -60.405 63.359 1 83.47 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #