data_4NMN # _model_server_result.job_id O2tg7uD4zPQQVfndSJ2YJQ _model_server_result.datetime_utc '2025-04-01 12:20:24' _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 4nmn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 4NMN # _exptl.entry_id 4NMN _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 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 90 _cell.entry_id 4NMN _cell.length_a 195.707 _cell.length_b 195.707 _cell.length_c 195.707 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NMN _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F 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 disulf ? disulf1 A SG CYS 3 A CYS 9 1_555 A SG CYS 35 A CYS 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A OE1 GLU 122 A GLU 128 1_555 E SR SR . A SR 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc2 A OG1 THR 207 A THR 213 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc3 A OE1 GLU 231 A GLU 237 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc4 A OE2 GLU 231 A GLU 237 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc5 C O1B ADP . A ADP 1001 1_555 D MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc6 B OG1 THR 207 B THR 213 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc7 F O3B ADP . B ADP 1001 1_555 G MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? # _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 4NMN _atom_sites.fract_transf_matrix[1][1] 0.00511 _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] 0.00511 _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] 0.00511 _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 C 2 ADP A 1 1001 1001 ADP ADP . D 3 MG A 1 1002 1002 MG MG . E 4 SR A 1 1003 1003 SR SR . F 2 ADP B 1 1001 1001 ADP ADP . G 3 MG B 1 1002 1002 MG MG . H 5 HOH A 1 1101 24 HOH HOH . H 5 HOH A 2 1102 36 HOH HOH . H 5 HOH A 3 1103 50 HOH HOH . H 5 HOH A 4 1104 51 HOH HOH . H 5 HOH A 5 1105 52 HOH HOH . H 5 HOH A 6 1106 53 HOH HOH . H 5 HOH A 7 1107 54 HOH HOH . H 5 HOH A 8 1108 56 HOH HOH . H 5 HOH A 9 1109 57 HOH HOH . H 5 HOH A 10 1110 58 HOH HOH . H 5 HOH A 11 1111 59 HOH HOH . I 5 HOH B 1 1101 15 HOH HOH . I 5 HOH B 2 1102 38 HOH HOH . I 5 HOH B 3 1103 44 HOH HOH . I 5 HOH B 4 1104 45 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 . . . C 2 11.526 6.234 -28.417 1 78.56 ? PB ADP 1001 A 1 HETATM 2 O O1B ADP . . . C 2 12.56 6.924 -27.57 1 79.65 ? O1B ADP 1001 A 1 HETATM 3 O O2B ADP . . . C 2 11.529 4.751 -28.277 1 78.59 ? O2B ADP 1001 A 1 HETATM 4 O O3B ADP . . . C 2 10.146 6.788 -28.301 1 77.84 ? O3B ADP 1001 A 1 HETATM 5 P PA ADP . . . C 2 13.031 5.704 -30.782 1 79.53 ? PA ADP 1001 A 1 HETATM 6 O O1A ADP . . . C 2 14.162 6.576 -31.25 1 78.65 ? O1A ADP 1001 A 1 HETATM 7 O O2A ADP . . . C 2 13.308 4.416 -30.076 1 80.98 ? O2A ADP 1001 A 1 HETATM 8 O O3A ADP . . . C 2 11.957 6.554 -29.935 1 68.52 ? O3A ADP 1001 A 1 HETATM 9 O O5' ADP . . . C 2 12.203 5.331 -32.084 1 99.97 ? O5' ADP 1001 A 1 HETATM 10 C C5' ADP . . . C 2 12.895 4.995 -33.274 1 99.36 ? C5' ADP 1001 A 1 HETATM 11 C C4' ADP . . . C 2 12.062 4.036 -34.103 1 98.23 ? C4' ADP 1001 A 1 HETATM 12 O O4' ADP . . . C 2 12.801 3.738 -35.272 1 97.65 ? O4' ADP 1001 A 1 HETATM 13 C C3' ADP . . . C 2 11.865 2.721 -33.377 1 98.04 ? C3' ADP 1001 A 1 HETATM 14 O O3' ADP . . . C 2 10.472 2.402 -33.281 1 98.92 ? O3' ADP 1001 A 1 HETATM 15 C C2' ADP . . . C 2 12.618 1.679 -34.178 1 96.76 ? C2' ADP 1001 A 1 HETATM 16 O O2' ADP . . . C 2 11.72 0.85 -34.909 1 95.72 ? O2' ADP 1001 A 1 HETATM 17 C C1' ADP . . . C 2 13.438 2.47 -35.164 1 97.41 ? C1' ADP 1001 A 1 HETATM 18 N N9 ADP . . . C 2 14.825 2.62 -34.651 1 98.06 ? N9 ADP 1001 A 1 HETATM 19 C C8 ADP . . . C 2 15.208 3.352 -33.594 1 98.16 ? C8 ADP 1001 A 1 HETATM 20 N N7 ADP . . . C 2 16.546 3.27 -33.391 1 98.21 ? N7 ADP 1001 A 1 HETATM 21 C C5 ADP . . . C 2 17.05 2.463 -34.341 1 98.11 ? C5 ADP 1001 A 1 HETATM 22 C C6 ADP . . . C 2 18.389 1.946 -34.719 1 97.37 ? C6 ADP 1001 A 1 HETATM 23 N N6 ADP . . . C 2 19.502 2.275 -34.03 1 97.03 ? N6 ADP 1001 A 1 HETATM 24 N N1 ADP . . . C 2 18.471 1.125 -35.779 1 97.41 ? N1 ADP 1001 A 1 HETATM 25 C C2 ADP . . . C 2 17.382 0.784 -36.481 1 97.74 ? C2 ADP 1001 A 1 HETATM 26 N N3 ADP . . . C 2 16.141 1.208 -36.205 1 97.97 ? N3 ADP 1001 A 1 HETATM 27 C C4 ADP . . . C 2 15.91 2.039 -35.166 1 98.18 ? C4 ADP 1001 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #