data_3EQG # _model_server_result.job_id gjUEboySgW079MR5-4br8w _model_server_result.datetime_utc '2024-11-25 01:44:23' _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 3eqg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2}' # _entry.id 3EQG # _exptl.entry_id 3EQG _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 120 _cell.entry_id 3EQG _cell.length_a 76 _cell.length_b 76 _cell.length_c 222.32 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EQG _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS monomeric 1 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 111.16 # _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 B O1B ADP . A ADP 2 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc2 B O2A ADP . A ADP 2 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc3 C MG MG . A MG 3 1_555 A OD1 ASN 162 A ASN 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc4 C MG MG . A MG 3 1_555 A OD2 ASP 175 A ASP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc5 C MG MG . A MG 3 1_555 G O HOH . A HOH 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc6 E NA NA . A NA 6 1_555 A OD1 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc7 E NA NA . A NA 6 1_555 A OD2 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc8 E NA NA . A NA 6 1_555 A OD1 ASP 103 A ASP 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? # _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 42 n n PB O2B ADP sing 43 n n PB O3B ADP sing 44 n n PB O3A ADP sing 45 n n O2B HOB2 ADP sing 46 n n O3B HOB3 ADP sing 47 n n PA O1A ADP doub 48 n n PA O2A ADP sing 49 n n PA O3A ADP sing 50 n n PA O5' ADP sing 51 n n O2A HOA2 ADP sing 52 n n O5' C5' ADP sing 53 n n C5' C4' ADP sing 54 n n C5' "H5'1" ADP sing 55 n n C5' "H5'2" ADP sing 56 n n C4' O4' ADP sing 57 n n C4' C3' ADP sing 58 n n C4' H4' ADP sing 59 n n O4' C1' ADP sing 60 n n C3' O3' ADP sing 61 n n C3' C2' ADP sing 62 n n C3' H3' ADP sing 63 n n O3' HO3' ADP sing 64 n n C2' O2' ADP sing 65 n n C2' C1' ADP sing 66 n n C2' H2' ADP sing 67 n n O2' HO2' ADP sing 68 n n C1' N9 ADP sing 69 n n C1' H1' ADP sing 70 n n N9 C8 ADP sing 71 n y N9 C4 ADP sing 72 n y C8 N7 ADP doub 73 n y C8 H8 ADP sing 74 n n N7 C5 ADP sing 75 n y C5 C6 ADP sing 76 n y C5 C4 ADP doub 77 n y C6 N6 ADP sing 78 n n C6 N1 ADP doub 79 n y N6 HN61 ADP sing 80 n n N6 HN62 ADP sing 81 n n N1 C2 ADP sing 82 n y C2 N3 ADP doub 83 n y C2 H2 ADP sing 84 n n N3 C4 ADP sing 85 n y # _atom_sites.entry_id 3EQG _atom_sites.fract_transf_matrix[1][1] 0.013158 _atom_sites.fract_transf_matrix[1][2] 0.007597 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015193 _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] 0.004498 _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 2 2 ADP ADP . C 3 MG A 1 3 3 MG MG . D 4 CA A 1 5 5 CA CA . E 5 NA A 1 6 6 NA NA . F 6 4BM A 1 1 1 4BM 4BM . G 7 HOH A 1 394 394 HOH HOH . G 7 HOH A 2 395 395 HOH HOH . G 7 HOH A 3 396 396 HOH HOH . G 7 HOH A 4 397 397 HOH HOH . G 7 HOH A 5 398 398 HOH HOH . G 7 HOH A 6 399 399 HOH HOH . G 7 HOH A 7 400 400 HOH HOH . G 7 HOH A 8 401 401 HOH HOH . G 7 HOH A 9 402 402 HOH HOH . G 7 HOH A 10 403 403 HOH HOH . G 7 HOH A 11 404 404 HOH HOH . G 7 HOH A 12 405 405 HOH HOH . G 7 HOH A 13 406 406 HOH HOH . G 7 HOH A 14 407 407 HOH HOH . G 7 HOH A 15 408 408 HOH HOH . G 7 HOH A 16 409 409 HOH HOH . G 7 HOH A 17 410 410 HOH HOH . G 7 HOH A 18 411 411 HOH HOH . G 7 HOH A 19 412 412 HOH HOH . G 7 HOH A 20 413 413 HOH HOH . G 7 HOH A 21 414 414 HOH HOH . G 7 HOH A 22 415 415 HOH HOH . G 7 HOH A 23 416 416 HOH HOH . G 7 HOH A 24 417 417 HOH HOH . G 7 HOH A 25 418 418 HOH HOH . G 7 HOH A 26 419 419 HOH HOH . G 7 HOH A 27 420 420 HOH HOH . G 7 HOH A 28 421 421 HOH HOH . G 7 HOH A 29 422 422 HOH HOH . G 7 HOH A 30 423 423 HOH HOH . G 7 HOH A 31 424 424 HOH HOH . G 7 HOH A 32 425 425 HOH HOH . G 7 HOH A 33 426 426 HOH HOH . G 7 HOH A 34 427 427 HOH HOH . G 7 HOH A 35 428 428 HOH HOH . G 7 HOH A 36 429 429 HOH HOH . G 7 HOH A 37 430 430 HOH HOH . G 7 HOH A 38 431 431 HOH HOH . G 7 HOH A 39 432 432 HOH HOH . G 7 HOH A 40 433 433 HOH HOH . G 7 HOH A 41 434 434 HOH HOH . G 7 HOH A 42 435 435 HOH HOH . G 7 HOH A 43 436 436 HOH HOH . G 7 HOH A 44 437 393 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 -9.994 61.815 32.555 1 55.79 ? PB ADP 2 A 1 HETATM 2 O O1B ADP . . . B 2 -8.532 61.832 32.301 1 53.46 ? O1B ADP 2 A 1 HETATM 3 O O2B ADP . . . B 2 -10.811 63.192 32.774 1 61.09 ? O2B ADP 2 A 1 HETATM 4 O O3B ADP . . . B 2 -10.78 60.424 32.449 1 52.76 ? O3B ADP 2 A 1 HETATM 5 P PA ADP . . . B 2 -8.534 62.128 35.011 1 52.24 ? PA ADP 2 A 1 HETATM 6 O O1A ADP . . . B 2 -8.572 61.527 36.366 1 55.65 ? O1A ADP 2 A 1 HETATM 7 O O2A ADP . . . B 2 -7.165 61.634 34.264 1 49.29 ? O2A ADP 2 A 1 HETATM 8 O O3A ADP . . . B 2 -9.912 61.636 34.206 1 56.48 ? O3A ADP 2 A 1 HETATM 9 O O5' ADP . . . B 2 -8.413 63.728 35.198 1 50.47 ? O5' ADP 2 A 1 HETATM 10 C C5' ADP . . . B 2 -9.678 64.36 35.108 1 51.95 ? C5' ADP 2 A 1 HETATM 11 C C4' ADP . . . B 2 -9.361 65.819 34.809 1 58.5 ? C4' ADP 2 A 1 HETATM 12 O O4' ADP . . . B 2 -8.108 66.154 35.465 1 61.5 ? O4' ADP 2 A 1 HETATM 13 C C3' ADP . . . B 2 -8.97 65.938 33.344 1 60.51 ? C3' ADP 2 A 1 HETATM 14 O O3' ADP . . . B 2 -10.126 66.004 32.509 1 59.94 ? O3' ADP 2 A 1 HETATM 15 C C2' ADP . . . B 2 -8.106 67.234 33.36 1 60.65 ? C2' ADP 2 A 1 HETATM 16 O O2' ADP . . . B 2 -8.878 68.394 33.182 1 62.39 ? O2' ADP 2 A 1 HETATM 17 C C1' ADP . . . B 2 -7.518 67.273 34.77 1 58.98 ? C1' ADP 2 A 1 HETATM 18 N N9 ADP . . . B 2 -6.048 67.159 34.723 1 54.78 ? N9 ADP 2 A 1 HETATM 19 C C8 ADP . . . B 2 -5.309 66.003 34.74 1 51.15 ? C8 ADP 2 A 1 HETATM 20 N N7 ADP . . . B 2 -4.035 66.276 34.618 1 47.04 ? N7 ADP 2 A 1 HETATM 21 C C5 ADP . . . B 2 -3.873 67.635 34.567 1 47.09 ? C5 ADP 2 A 1 HETATM 22 C C6 ADP . . . B 2 -2.77 68.505 34.465 1 45.51 ? C6 ADP 2 A 1 HETATM 23 N N6 ADP . . . B 2 -1.49 68.011 34.392 1 45.64 ? N6 ADP 2 A 1 HETATM 24 N N1 ADP . . . B 2 -2.983 69.821 34.443 1 49.81 ? N1 ADP 2 A 1 HETATM 25 C C2 ADP . . . B 2 -4.214 70.316 34.443 1 52.61 ? C2 ADP 2 A 1 HETATM 26 N N3 ADP . . . B 2 -5.285 69.54 34.525 1 51.84 ? N3 ADP 2 A 1 HETATM 27 C C4 ADP . . . B 2 -5.161 68.209 34.614 1 50.96 ? C4 ADP 2 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #