data_2O39 # _model_server_result.job_id 4bKum01XpgsS8q_NTN8hCA _model_server_result.datetime_utc '2025-03-22 02:44:24' _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 2o39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":3081}' # _entry.id 2O39 # _exptl.entry_id 2O39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 3 _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 2O39 _cell.length_a 106.14 _cell.length_b 106.14 _cell.length_c 68.32 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2O39 _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 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,C,E,G,J,L 1 1,2,3 B,D,F,H,I,K,M 2 1,4,5 # 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' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 53.07 91.919936 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -53.07 91.919936 0 4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 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 ? 4 G N N ? 4 H N N ? 4 I N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E NAG 1 E 1 NAG S 1080 NAG 3 n E NAG 2 E 2 NAG S 2080 NAG 3 n E BMA 3 E 3 BMA S 3080 BMA 3 n F NAG 1 F 1 NAG Z 1080 NAG 3 n F NAG 2 F 2 NAG Z 2080 NAG 3 n F BMA 3 F 3 BMA Z 3080 BMA # 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 C SG CYS 1 C CYS 1 1_555 C SG CYS 46 C CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 C SG CYS 30 C CYS 30 1_555 C SG CYS 60 C CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 C SG CYS 65 C CYS 65 1_555 C SG CYS 107 C CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 C SG CYS 93 C CYS 93 1_555 C SG CYS 123 C CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf5 D SG CYS 1 D CYS 1 1_555 D SG CYS 46 D CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 0.788 ? disulf ? disulf6 D SG CYS 30 D CYS 30 1_555 D SG CYS 60 D CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 D SG CYS 65 D CYS 65 1_555 D SG CYS 107 D CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 D SG CYS 93 D CYS 93 1_555 D SG CYS 123 D CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? covale ? covale1 C ND2 ASN 80 C ASN 80 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 D ND2 ASN 80 D ASN 80 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale4 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale5 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale6 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? metalc ? metalc1 C OD2 ASP 57 C ASP 57 1_555 G CA CA . C CA 3081 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc2 C OD1 ASP 58 C ASP 58 1_555 G CA CA . C CA 3081 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.829 ? metalc ? metalc3 C OD1 ASP 70 C ASP 70 1_546 I CA CA . D CA 3082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc4 C OD2 ASP 70 C ASP 70 1_546 I CA CA . D CA 3082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.254 ? metalc ? metalc5 C O ALA 76 C ALA 76 1_546 I CA CA . D CA 3082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.041 ? metalc ? metalc6 D OD1 ASP 57 D ASP 57 1_555 H CA CA . D CA 3081 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc7 D OD1 ASP 58 D ASP 58 1_555 H CA CA . D CA 3081 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? metalc ? metalc8 D OD1 ASP 70 D ASP 70 1_555 I CA CA . D CA 3082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc9 D O ALA 76 D ALA 76 1_555 I CA CA . D CA 3082 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2O39 _atom_sites.fract_transf_matrix[1][1] 0.009422 _atom_sites.fract_transf_matrix[1][2] 0.00544 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010879 _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] 0.014637 _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 G 4 CA C 1 3081 101 CA CA . H 4 CA D 1 3081 102 CA CA . I 4 CA D 1 3082 103 CA CA . J 5 HOH A 1 1 1 HOH HOH . J 5 HOH A 2 7 7 HOH HOH . J 5 HOH A 3 9 9 HOH HOH . J 5 HOH A 4 11 11 HOH HOH . J 5 HOH A 5 12 12 HOH HOH . J 5 HOH A 6 16 16 HOH HOH . J 5 HOH A 7 19 19 HOH HOH . J 5 HOH A 8 22 22 HOH HOH . J 5 HOH A 9 24 24 HOH HOH . J 5 HOH A 10 25 25 HOH HOH . J 5 HOH A 11 27 27 HOH HOH . J 5 HOH A 12 30 30 HOH HOH . J 5 HOH A 13 31 31 HOH HOH . K 5 HOH B 1 2 2 HOH HOH . K 5 HOH B 2 5 5 HOH HOH . K 5 HOH B 3 8 8 HOH HOH . K 5 HOH B 4 14 14 HOH HOH . K 5 HOH B 5 15 15 HOH HOH . K 5 HOH B 6 20 20 HOH HOH . K 5 HOH B 7 21 21 HOH HOH . K 5 HOH B 8 33 33 HOH HOH . K 5 HOH B 9 34 34 HOH HOH . L 5 HOH C 1 3082 3 HOH HOH . L 5 HOH C 2 3083 4 HOH HOH . L 5 HOH C 3 3084 6 HOH HOH . L 5 HOH C 4 3085 10 HOH HOH . L 5 HOH C 5 3086 13 HOH HOH . L 5 HOH C 6 3087 28 HOH HOH . L 5 HOH C 7 3088 32 HOH HOH . M 5 HOH D 1 3083 17 HOH HOH . M 5 HOH D 2 3084 18 HOH HOH . M 5 HOH D 3 3085 23 HOH HOH . M 5 HOH D 4 3086 26 HOH HOH . M 5 HOH D 5 3087 29 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id G _atom_site.label_entity_id 4 _atom_site.Cartn_x -32.723 _atom_site.Cartn_y 33.031 _atom_site.Cartn_z -5.001 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 54.52 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 3081 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 1 #