data_8YU9 # _model_server_result.job_id OhH21WlkahFwkpdnfusjeQ _model_server_result.datetime_utc '2024-10-18 06:13:21' _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 8yu9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":502}' # _entry.id 8YU9 # _exptl.entry_id 8YU9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _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 8YU9 _cell.length_a 104.974 _cell.length_b 157.379 _cell.length_c 182.635 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YU9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 6 H N N ? 6 P 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 B NH2 ARG 251 B ARG 251 1_555 L O3S MES . B MES 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? metalc ? metalc1 A OD2 ASP 39 A ASP 39 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc2 A OG1 THR 41 A THR 41 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 A O GLY 44 A GLY 44 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc4 A OD2 ASP 47 A ASP 47 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc5 A OD1 ASN 50 A ASN 50 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 H CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc7 A OE2 GLU 71 A GLU 71 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 I MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 N MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc11 B OD2 ASP 177 B ASP 177 1_555 N MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc12 K O2A GDP . B GDP 502 1_555 N MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc15 C OG1 THR 41 C THR 41 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc16 C OD2 ASP 47 C ASP 47 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 P CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc18 O O3G GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc19 O O2B GTP . C GTP 501 1_555 Q MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? # _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 8YU9 _atom_sites.fract_transf_matrix[1][1] 0.009526 _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] 0.006354 _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] 0.005475 _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 5 GTP A 1 501 501 GTP GTP . H 6 CA A 1 502 502 CA CA . I 7 MG A 1 503 503 MG MG . J 8 A1D7A B 1 501 505 A1D7A LIG . K 9 GDP B 1 502 501 GDP GDP . L 10 MES B 1 503 502 MES MES . M 10 MES B 1 504 503 MES MES . N 7 MG B 1 505 504 MG MG . O 5 GTP C 1 501 501 GTP GTP . P 6 CA C 1 502 502 CA CA . Q 7 MG C 1 503 503 MG MG . R 8 A1D7A D 1 501 502 A1D7A LIG . S 9 GDP D 1 502 501 GDP GDP . T 11 ACP F 1 401 401 ACP ACP . # _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 P _atom_site.label_entity_id 6 _atom_site.Cartn_x 13.63 _atom_site.Cartn_y -54.54 _atom_site.Cartn_z 10.136 _atom_site.occupancy 0 _atom_site.B_iso_or_equiv 75.16 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 502 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #