data_3B5Z # _model_server_result.job_id NxhuEMJsaKoKelW6yLjuSQ _model_server_result.datetime_utc '2025-01-02 18:32:48' _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 3b5z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":601}' # _entry.id 3B5Z # _exptl.entry_id 3B5Z _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 121.57 _cell.angle_gamma 90 _cell.entry_id 3B5Z _cell.length_a 267.169 _cell.length_b 121.103 _cell.length_c 176.744 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B5Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_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,E,F,G,H 1 1 C,D,I,J,K,L 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K 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 covale ? covale1 E PB ADP . A ADP 5001 1_555 F O1 VO4 . A VO4 5002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.538 ? covale ? covale2 G PB ADP . B ADP 601 1_555 H O1 VO4 . B VO4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.581 ? covale ? covale3 I PB ADP . C ADP 601 1_555 J O1 VO4 . C VO4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.542 ? covale ? covale4 K PB ADP . D ADP 601 1_555 L O1 VO4 . D VO4 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.543 ? # _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 3B5Z _atom_sites.fract_transf_matrix[1][1] 0.003743 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0023 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008257 _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] 0.006641 _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 E 2 ADP A 1 5001 5001 ADP ADP . F 3 VO4 A 1 5002 5005 VO4 VO4 . G 2 ADP B 1 601 5002 ADP ADP . H 3 VO4 B 1 602 5006 VO4 VO4 . I 2 ADP C 1 601 5003 ADP ADP . J 3 VO4 C 1 602 5007 VO4 VO4 . K 2 ADP D 1 601 5004 ADP ADP . L 3 VO4 D 1 602 5008 VO4 VO4 . # 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 . . . I 2 -104.782 41.426 -20.222 1 156.27 ? PB ADP 601 C 1 HETATM 2 O O1B ADP . . . I 2 -104.269 41.3 -21.565 1 156.27 ? O1B ADP 601 C 1 HETATM 3 O O2B ADP . . . I 2 -104.524 40.413 -19.032 1 156.27 ? O2B ADP 601 C 1 HETATM 4 P PA ADP . . . I 2 -102.133 41.008 -20.109 1 156.27 ? PA ADP 601 C 1 HETATM 5 O O1A ADP . . . I 2 -102.312 39.786 -19.288 1 156.27 ? O1A ADP 601 C 1 HETATM 6 O O2A ADP . . . I 2 -102.107 40.62 -21.672 1 156.27 ? O2A ADP 601 C 1 HETATM 7 O O3A ADP . . . I 2 -103.34 42.048 -19.825 1 156.27 ? O3A ADP 601 C 1 HETATM 8 O O5' ADP . . . I 2 -100.693 41.652 -19.742 1 156.27 ? O5' ADP 601 C 1 HETATM 9 C C5' ADP . . . I 2 -99.729 40.639 -20.119 1 156.27 ? C5' ADP 601 C 1 HETATM 10 C C4' ADP . . . I 2 -98.277 41.059 -19.865 1 156.27 ? C4' ADP 601 C 1 HETATM 11 O O4' ADP . . . I 2 -98.058 41.292 -18.445 1 156.27 ? O4' ADP 601 C 1 HETATM 12 C C3' ADP . . . I 2 -97.329 39.939 -20.32 1 156.27 ? C3' ADP 601 C 1 HETATM 13 O O3' ADP . . . I 2 -96.37 40.425 -21.272 1 156.27 ? O3' ADP 601 C 1 HETATM 14 C C2' ADP . . . I 2 -96.665 39.385 -19.043 1 156.27 ? C2' ADP 601 C 1 HETATM 15 O O2' ADP . . . I 2 -95.236 39.48 -19.125 1 156.27 ? O2' ADP 601 C 1 HETATM 16 C C1' ADP . . . I 2 -97.238 40.221 -17.873 1 156.27 ? C1' ADP 601 C 1 HETATM 17 N N9 ADP . . . I 2 -98.033 39.382 -16.922 1 156.27 ? N9 ADP 601 C 1 HETATM 18 C C8 ADP . . . I 2 -99.389 39.182 -16.925 1 156.27 ? C8 ADP 601 C 1 HETATM 19 N N7 ADP . . . I 2 -99.737 38.402 -15.961 1 156.27 ? N7 ADP 601 C 1 HETATM 20 C C5 ADP . . . I 2 -98.649 38.046 -15.277 1 156.27 ? C5 ADP 601 C 1 HETATM 21 C C6 ADP . . . I 2 -98.415 37.236 -14.165 1 156.27 ? C6 ADP 601 C 1 HETATM 22 N N6 ADP . . . I 2 -99.464 36.603 -13.55 1 156.27 ? N6 ADP 601 C 1 HETATM 23 N N1 ADP . . . I 2 -97.164 37.085 -13.72 1 156.27 ? N1 ADP 601 C 1 HETATM 24 C C2 ADP . . . I 2 -96.146 37.686 -14.307 1 156.27 ? C2 ADP 601 C 1 HETATM 25 N N3 ADP . . . I 2 -96.319 38.463 -15.364 1 156.27 ? N3 ADP 601 C 1 HETATM 26 C C4 ADP . . . I 2 -97.536 38.669 -15.874 1 156.27 ? C4 ADP 601 C 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 26 #