data_6G3S # _model_server_result.job_id CZLhXPX8z2bESrwmfsB_dQ _model_server_result.datetime_utc '2024-10-19 03:41:36' _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 6g3s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6G3S # _exptl.entry_id 6G3S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 6G3S _cell.length_a 69.9 _cell.length_b 70.967 _cell.length_c 99.295 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6G3S _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _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 # 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 A OD2 ASP 8 A ASP 10 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc2 A O TYR 13 A TYR 15 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc3 A OD1 ASP 197 A ASP 199 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc4 A O THR 202 A THR 204 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? metalc ? metalc5 A OG1 THR 202 A THR 204 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc6 A OG1 THR 202 A THR 204 1_555 G NA NA . A NA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc7 A NH2 ARG 270 A ARG 272 1_555 I W6 TEW . A TEW 408 3_554 ? ? ? ? B ? ? ? ? ? ? ? 3.195 ? metalc ? metalc8 B O2B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.756 ? metalc ? metalc9 B O2B ADP . A ADP 401 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc10 B O3A ADP . A ADP 401 1_555 F NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc11 B O1B ADP . A ADP 401 1_555 G NA NA . A NA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc12 C MG MG . A MG 402 1_555 D O1 PO4 . A PO4 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc13 C MG MG . A MG 402 1_555 J O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc14 C MG MG . A MG 402 1_555 J O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc15 C MG MG . A MG 402 1_555 J O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc16 C MG MG . A MG 402 1_555 J O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc17 D O1 PO4 . A PO4 403 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc18 D O3 PO4 . A PO4 403 1_555 G NA NA . A NA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc19 E NA NA . A NA 404 1_555 J O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc20 F NA NA . A NA 405 1_555 J O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc21 F NA NA . A NA 405 1_555 J O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? # _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 6G3S _atom_sites.fract_transf_matrix[1][1] 0.014306 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014091 _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] 0.010071 _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 B 2 ADP A 1 401 1 ADP ADP . C 3 MG A 1 402 1 MG MG . D 4 PO4 A 1 403 1 PO4 PO4 . E 5 NA A 1 404 1 NA NA . F 5 NA A 1 405 2 NA NA . G 5 NA A 1 406 3 NA NA . H 6 TEW A 1 407 1 TEW TEW . I 6 TEW A 1 408 2 TEW TEW . J 7 HOH A 1 501 9 HOH HOH . J 7 HOH A 2 502 11 HOH HOH . J 7 HOH A 3 503 1 HOH HOH . J 7 HOH A 4 504 2 HOH HOH . J 7 HOH A 5 505 4 HOH HOH . J 7 HOH A 6 506 12 HOH HOH . J 7 HOH A 7 507 8 HOH HOH . J 7 HOH A 8 508 5 HOH HOH . J 7 HOH A 9 509 3 HOH HOH . J 7 HOH A 10 510 10 HOH HOH . J 7 HOH A 11 511 7 HOH HOH . J 7 HOH A 12 512 6 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 . . . B 2 -8.408 8.092 -14.981 1 30.13 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -7.964 6.783 -15.428 1 37.88 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -9.887 8.296 -15.242 1 31.84 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -7.906 8.336 -13.611 1 33.6 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -7.23 8.876 -17.504 1 30.15 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -6.894 10.181 -18.125 1 26.97 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -8.301 8.013 -18.11 1 32.29 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -7.58 9.11 -15.933 1 32.37 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -5.981 7.932 -17.481 1 30.62 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -4.708 8.454 -17.19 1 34.09 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -3.7 7.323 -17.456 1 37.39 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -3.514 7.245 -18.878 1 36.67 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -2.313 7.506 -16.804 1 35.81 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -1.692 6.273 -16.377 1 31.17 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -1.546 8.072 -17.975 1 36.49 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -0.171 7.786 -17.859 1 36.59 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -2.146 7.319 -19.171 1 35.83 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -1.863 7.993 -20.463 1 36.1 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -2.123 9.273 -20.832 1 34.69 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -1.689 9.522 -22.073 1 29.47 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -1.135 8.384 -22.505 1 35.14 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -0.422 7.93 -23.717 1 34.46 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -0.271 8.757 -24.753 1 34.39 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 0.038 6.668 -23.744 1 37.39 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -0.093 5.794 -22.731 1 36.04 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -0.721 6.138 -21.599 1 37.8 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -1.243 7.382 -21.446 1 35.35 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 27 #