data_5GSZ # _model_server_result.job_id wtlpGbwLcvBEehyk_vncoQ _model_server_result.datetime_utc '2024-12-21 15:50:22' _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 5gsz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5GSZ # _exptl.entry_id 5GSZ _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 5GSZ _cell.length_a 122.604 _cell.length_b 122.604 _cell.length_c 56.198 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GSZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42 21 2' # _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 _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 covale ? covale1 A C SER 175 A SER 175 1_555 A NH1 ARG 204 A ARG 204 4_455 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? metalc ? metalc1 A OG1 THR 111 A THR 111 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc2 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc3 C MG MG . A MG 402 1_555 D O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc4 C MG MG . A MG 402 1_555 D O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc5 C MG MG . A MG 402 1_555 D O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc6 C MG MG . A MG 402 1_555 D O HOH . A HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? # _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 5GSZ _atom_sites.fract_transf_matrix[1][1] 0.008156 _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] 0.008156 _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] 0.017794 _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 1 401 401 ADP ADP . C 3 MG A 1 402 402 MG MG . D 4 HOH A 1 501 501 HOH HOH . D 4 HOH A 2 502 502 HOH HOH . D 4 HOH A 3 503 503 HOH HOH . D 4 HOH A 4 504 504 HOH HOH . D 4 HOH A 5 505 505 HOH HOH . D 4 HOH A 6 506 506 HOH HOH . D 4 HOH A 7 507 507 HOH HOH . D 4 HOH A 8 508 508 HOH HOH . D 4 HOH A 9 509 509 HOH HOH . D 4 HOH A 10 510 510 HOH HOH . D 4 HOH A 11 511 511 HOH HOH . D 4 HOH A 12 512 512 HOH HOH . D 4 HOH A 13 513 513 HOH HOH . D 4 HOH A 14 514 514 HOH HOH . D 4 HOH A 15 515 515 HOH HOH . D 4 HOH A 16 516 516 HOH HOH . D 4 HOH A 17 517 517 HOH HOH . D 4 HOH A 18 518 518 HOH HOH . D 4 HOH A 19 519 519 HOH HOH . D 4 HOH A 20 520 520 HOH HOH . D 4 HOH A 21 521 521 HOH HOH . D 4 HOH A 22 522 522 HOH HOH . D 4 HOH A 23 523 523 HOH HOH . D 4 HOH A 24 524 524 HOH HOH . D 4 HOH A 25 525 525 HOH HOH . D 4 HOH A 26 526 526 HOH HOH . D 4 HOH A 27 527 527 HOH HOH . D 4 HOH A 28 528 528 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 12.732 34.428 19.138 1 40.77 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 11.725 35.555 19.167 1 39.98 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 12.136 33.157 19.695 1 39.31 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 14.105 34.806 19.625 1 40.17 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 12.709 35.271 16.465 1 38.65 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 11.37 35.024 15.841 1 36.55 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 13.057 36.598 17.09 1 39.03 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 13.001 34.123 17.574 1 43.22 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 13.882 35.077 15.389 1 49.43 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 13.912 34.052 14.411 1 45.96 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 14.394 34.685 13.123 1 41.42 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 13.91 33.865 12.068 1 43.84 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 13.705 36.013 12.953 1 42.03 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 14.506 36.756 12.033 1 50.56 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 12.37 35.65 12.339 1 41.22 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 11.927 36.672 11.436 1 47.3 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 12.668 34.365 11.574 1 43.25 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 11.621 33.333 11.778 1 42.83 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 11.262 32.774 12.955 1 43.79 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 10.277 31.847 12.804 1 42.52 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 9.991 31.813 11.491 1 38.65 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 9.04 31.073 10.654 1 39.4 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 8.197 30.163 11.204 1 44.66 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 9.05 31.336 9.329 1 41.33 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 9.895 32.226 8.785 1 41.54 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 10.776 32.952 9.493 1 42.11 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 10.871 32.788 10.824 1 40.16 ? C4 ADP 401 A 1 HETATM 28 H "H5'1" ADP . . . B 2 13.031 33.663 14.294 1 45.96 ? "H5'1" ADP 401 A 1 HETATM 29 H "H5'2" ADP . . . B 2 14.505 33.334 14.684 1 45.96 ? "H5'2" ADP 401 A 1 HETATM 30 H H4' ADP . . . B 2 15.359 34.783 13.127 1 41.42 ? H4' ADP 401 A 1 HETATM 31 H H3' ADP . . . B 2 13.587 36.533 13.763 1 42.03 ? H3' ADP 401 A 1 HETATM 32 H HO3' ADP . . . B 2 14.032 37.004 11.386 1 50.56 ? HO3' ADP 401 A 1 HETATM 33 H H2' ADP . . . B 2 11.669 35.55 13.001 1 41.22 ? H2' ADP 401 A 1 HETATM 34 H HO2' ADP . . . B 2 11.126 36.533 11.227 1 47.3 ? HO2' ADP 401 A 1 HETATM 35 H H1' ADP . . . B 2 12.697 34.561 10.624 1 43.25 ? H1' ADP 401 A 1 HETATM 36 H H8 ADP . . . B 2 11.66 33.007 13.808 1 43.79 ? H8 ADP 401 A 1 HETATM 37 H HN61 ADP . . . B 2 8.217 30.015 12.051 1 44.66 ? HN61 ADP 401 A 1 HETATM 38 H HN62 ADP . . . B 2 7.643 29.734 10.706 1 44.66 ? HN62 ADP 401 A 1 HETATM 39 H H2 ADP . . . B 2 9.868 32.352 7.824 1 41.54 ? H2 ADP 401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #