data_3JB3 # _model_server_result.job_id RiVZPKvnns3MyaE6E855tg _model_server_result.datetime_utc '2024-11-15 05:47:08' _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 3jb3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1105}' # _entry.id 3JB3 # _exptl.entry_id 3JB3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 24.305 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _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 3JB3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JB3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? 300-MERIC 300 'complete icosahedral assembly' 1 ? pentameric 5 'icosahedral asymmetric unit' 2 ? 25-meric 25 'icosahedral pentamer' 3 ? 30-meric 30 'icosahedral 23 hexamer' 4 ? pentameric 5 'icosahedral asymmetric unit, std point frame' 5 # 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,H,I,J 1 (1-60) A,B,C,D,E,F,G,H,I,J 2 1 A,B,C,D,E,F,G,H,I,J 3 (1-5) A,B,C,D,E,F,G,H,I,J 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H,I,J 5 P # 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] P 'transform to point frame' ? ? 0.587785 -0.809017 0 0.688191 0.5 0.525731 -0.425326 -0.309017 0.850651 -0.00003 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.309017 -0.951057 0 0.951057 0.309017 0 0 0 1 -0.00001 -0.00003 0 3 'point symmetry operation' ? ? -0.809017 -0.587785 0 0.587785 -0.809017 0 0 0 1 0.00002 -0.00005 0 4 'point symmetry operation' ? ? -0.809017 0.587785 0 -0.587785 -0.809017 0 0 0 1 0.00005 -0.00003 0 5 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 0 0 0 1 0.00004 0 0 6 'point symmetry operation' ? ? -0.638196 0.262866 -0.723607 0.262866 -0.809017 -0.525731 -0.723607 -0.525731 0.447213 0.00004 -0.00005 0 7 'point symmetry operation' ? ? 0.052787 0.688191 -0.723607 -0.688191 -0.5 -0.525731 -0.723607 0.525731 0.447213 0.00003 -0.00002 0.00003 8 'point symmetry operation' ? ? 0.67082 0.16246 -0.723607 -0.688191 0.5 -0.525731 0.276393 0.850651 0.447214 0 0 0.00002 9 'point symmetry operation' ? ? 0.361803 -0.587785 -0.723607 0.262866 0.809017 -0.525731 0.894427 0 0.447214 0 0 -0.00002 10 'point symmetry operation' ? ? -0.447214 -0.525731 -0.723607 0.850651 0 -0.525731 0.276393 -0.850651 0.447214 0.00001 -0.00004 -0.00003 11 'point symmetry operation' ? ? -0.052787 0.688191 0.723607 0.688191 -0.5 0.525731 0.723607 0.525731 -0.447213 0.00004 -0.00005 0 12 'point symmetry operation' ? ? 0.638196 0.262866 0.723607 -0.262866 -0.809017 0.525731 0.723607 -0.525731 -0.447213 0.00001 -0.00004 -0.00003 13 'point symmetry operation' ? ? 0.447214 -0.525731 0.723607 -0.850651 0 0.525731 -0.276393 -0.850651 -0.447214 0 0 -0.00002 14 'point symmetry operation' ? ? -0.361803 -0.587785 0.723607 -0.262866 0.809017 0.525731 -0.894427 0 -0.447214 0 0 0.00002 15 'point symmetry operation' ? ? -0.67082 0.16246 0.723607 0.688191 0.5 0.525731 -0.276393 0.850651 -0.447214 0.00003 -0.00002 0.00003 16 'point symmetry operation' ? ? -0.309017 -0.951057 0 -0.951057 0.309017 0 0 0 -1 0 0 0 17 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0.00004 0 0 18 'point symmetry operation' ? ? -0.309017 0.951057 0 0.951057 0.309017 0 0 0 -1 0.00005 -0.00003 0 19 'point symmetry operation' ? ? 0.809017 0.587785 0 0.587785 -0.809017 0 0 0 -1 0.00002 -0.00005 0 20 'point symmetry operation' ? ? 0.809017 -0.587785 0 -0.587785 -0.809017 0 0 0 -1 -0.00001 -0.00003 0 21 'point symmetry operation' ? ? -0.138197 -0.951057 0.276393 0.425326 -0.309017 -0.850651 0.894427 0 0.447214 0 -0.00004 -0.00002 22 'point symmetry operation' ? ? -0.947214 -0.16246 0.276393 -0.16246 -0.5 -0.850651 0.276393 -0.850651 0.447214 0.00003 -0.00003 -0.00003 23 'point symmetry operation' ? ? -0.447214 0.850651 0.276393 -0.525731 0 -0.850651 -0.723607 -0.525731 0.447214 0.00005 -0.00002 0 24 'point symmetry operation' ? ? 0.67082 0.688191 0.276393 -0.16246 0.5 -0.850651 -0.723607 0.525731 0.447214 0.00002 0 0.00003 25 'point symmetry operation' ? ? 0.861803 -0.425326 0.276393 0.425326 0.309017 -0.850651 0.276393 0.850651 0.447214 0 -0.00002 0.00002 26 'point symmetry operation' ? ? -0.361803 0.587785 0.723607 0.262866 0.809017 -0.525731 -0.894427 0 -0.447214 0.00004 0 0.00002 27 'point symmetry operation' ? ? 0.447214 0.525731 0.723607 0.850651 0 -0.525731 -0.276393 0.850651 -0.447214 0.00002 -0.00004 0.00003 28 'point symmetry operation' ? ? 0.638196 -0.262866 0.723607 0.262866 -0.809017 -0.525731 0.723607 0.525731 -0.447213 0 -0.00005 0 29 'point symmetry operation' ? ? -0.052787 -0.688191 0.723607 -0.688191 -0.5 -0.525731 0.723607 -0.525731 -0.447213 0 -0.00002 -0.00003 30 'point symmetry operation' ? ? -0.67082 -0.16246 0.723607 -0.688191 0.5 -0.525731 -0.276393 -0.850651 -0.447214 0.00003 0 -0.00002 31 'point symmetry operation' ? ? -0.447214 0.525731 -0.723607 -0.850651 0 0.525731 0.276393 0.850651 0.447214 0.00004 0 0.00002 32 'point symmetry operation' ? ? 0.361803 0.587785 -0.723607 -0.262866 0.809017 0.525731 0.894427 0 0.447214 0.00003 0 -0.00002 33 'point symmetry operation' ? ? 0.67082 -0.16246 -0.723607 0.688191 0.5 0.525731 0.276393 -0.850651 0.447214 0 -0.00002 -0.00003 34 'point symmetry operation' ? ? 0.052787 -0.688191 -0.723607 0.688191 -0.5 0.525731 -0.723607 -0.525731 0.447213 0 -0.00005 0 35 'point symmetry operation' ? ? -0.638196 -0.262866 -0.723607 -0.262866 -0.809017 0.525731 -0.723607 0.525731 0.447213 0.00002 -0.00004 0.00003 36 'point symmetry operation' ? ? 0.947214 -0.16246 -0.276393 0.16246 -0.5 0.850651 -0.276393 -0.850651 -0.447214 0 -0.00004 -0.00002 37 'point symmetry operation' ? ? 0.138197 -0.951057 -0.276393 -0.425326 -0.309017 0.850651 -0.894427 0 -0.447214 0 -0.00002 0.00002 38 'point symmetry operation' ? ? -0.861803 -0.425326 -0.276393 -0.425326 0.309017 0.850651 -0.276393 0.850651 -0.447214 0.00002 0 0.00003 39 'point symmetry operation' ? ? -0.67082 0.688191 -0.276393 0.16246 0.5 0.850651 0.723607 0.525731 -0.447214 0.00005 -0.00002 0 40 'point symmetry operation' ? ? 0.447214 0.850651 -0.276393 0.525731 0 0.850651 0.723607 -0.525731 -0.447214 0.00003 -0.00003 -0.00003 41 'point symmetry operation' ? ? -0.138197 0.425326 0.894427 -0.951057 -0.309017 0 0.276393 -0.850651 0.447214 0.00003 -0.00002 -0.00003 42 'point symmetry operation' ? ? 0.361803 0.262866 0.894427 -0.587785 0.809017 0 -0.723607 -0.525731 0.447214 0.00002 0 0 43 'point symmetry operation' ? ? 0.361803 -0.262866 0.894427 0.587785 0.809017 0 -0.723607 0.525731 0.447214 0 -0.00001 0.00003 44 'point symmetry operation' ? ? -0.138197 -0.425325 0.894427 0.951057 -0.309017 0 0.276393 0.850651 0.447214 0 -0.00005 0.00002 45 'point symmetry operation' ? ? -0.447214 0 0.894427 0 -1 0 0.894427 0 0.447214 0.00003 -0.00005 -0.00002 46 'point symmetry operation' ? ? -0.447214 -0.850651 0.276393 0.525731 0 0.850651 -0.723607 0.525731 0.447214 0 -0.00003 0.00003 47 'point symmetry operation' ? ? -0.947214 0.16246 0.276393 0.16246 -0.5 0.850651 0.276393 0.850651 0.447214 0.00004 -0.00004 0.00002 48 'point symmetry operation' ? ? -0.138197 0.951057 0.276393 -0.425325 -0.309017 0.850651 0.894427 0 0.447214 0.00004 -0.00002 -0.00002 49 'point symmetry operation' ? ? 0.861803 0.425326 0.276393 -0.425326 0.309017 0.850651 0.276393 -0.850651 0.447214 0.00001 0 -0.00003 50 'point symmetry operation' ? ? 0.67082 -0.688191 0.276393 0.16246 0.5 0.850651 -0.723607 -0.525731 0.447214 -0.00001 -0.00001 0 51 'point symmetry operation' ? ? 0.947214 0.16246 -0.276393 -0.16246 -0.5 -0.850651 -0.276393 0.850651 -0.447214 0 -0.00003 0.00003 52 'point symmetry operation' ? ? 0.447214 -0.850651 -0.276393 -0.525731 0 -0.850651 0.723607 0.525731 -0.447214 -0.00001 -0.00001 0 53 'point symmetry operation' ? ? -0.67082 -0.688191 -0.276393 -0.16246 0.5 -0.850651 0.723607 -0.525731 -0.447214 0.00001 0 -0.00003 54 'point symmetry operation' ? ? -0.861803 0.425326 -0.276393 0.425326 0.309017 -0.850651 -0.276393 -0.850651 -0.447214 0.00004 -0.00002 -0.00002 55 'point symmetry operation' ? ? 0.138197 0.951057 -0.276393 0.425326 -0.309017 -0.850651 -0.894427 0 -0.447214 0.00004 -0.00004 0.00002 56 'point symmetry operation' ? ? -0.361803 0.262866 -0.894427 0.587785 0.809017 0 0.723607 -0.525731 -0.447214 0.00003 -0.00002 -0.00003 57 'point symmetry operation' ? ? 0.138197 0.425326 -0.894427 0.951057 -0.309017 0 -0.276393 -0.850651 -0.447214 0.00003 -0.00005 -0.00002 58 'point symmetry operation' ? ? 0.447214 0 -0.894427 0 -1 0 -0.894427 0 -0.447214 0 -0.00005 0.00002 59 'point symmetry operation' ? ? 0.138197 -0.425326 -0.894427 -0.951057 -0.309017 0 -0.276393 0.850651 -0.447214 0 -0.00001 0.00003 60 'point symmetry operation' ? ? -0.361803 -0.262866 -0.894427 -0.587785 0.809017 0 0.723607 0.525731 -0.447214 0.00002 0 0 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id J _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 I O2B GTP . A GTP 1104 1_555 J MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc2 I O3G GTP . A GTP 1104 1_555 J MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3JB3 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 4 SAM A 1 1101 0 SAM SAM . G 4 SAM A 1 1102 0 SAM SAM . H 5 ATP A 1 1103 701 ATP ATP . I 6 GTP A 1 1104 4034 GTP GTP . J 7 MG A 1 1105 1 MG MG . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id J _atom_site.label_entity_id 7 _atom_site.Cartn_x -47.787 _atom_site.Cartn_y -18.62 _atom_site.Cartn_z 284.951 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 194.87 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 1105 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 95 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 1 #