data_3VNU # _model_server_result.job_id 0e6cAfHEJrxdJFcvCtVMQQ _model_server_result.datetime_utc '2024-11-15 05:59:35' _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 3vnu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2503}' # _entry.id 3VNU # _exptl.entry_id 3VNU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 5 _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 3VNU _cell.length_a 139.005 _cell.length_b 255.506 _cell.length_c 101.425 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VNU _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 5 E N N ? 5 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 metalc ? metalc1 A OD1 ASP 968 A ASP 968 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc2 A OD1 ASP 968 A ASP 968 1_555 F CA CA . A CA 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc3 A O LEU 969 A LEU 969 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc4 A OD2 ASP 1053 A ASP 1053 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc5 A OD1 ASP 1053 A ASP 1053 1_555 F CA CA . A CA 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc6 D O2A ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc7 D O2B ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc8 D O2G ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.985 ? metalc ? metalc9 D O3B ATP . A ATP 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.176 ? hydrog WATSON-CRICK hydrog1 B N3 C 3 G C 2003 1_555 C N1 G 6 T G 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 C 3 G C 2003 1_555 C O6 G 6 T G 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 C 3 G C 2003 1_555 C N2 G 6 T G 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 U 4 G U 2004 1_555 C N1 A 5 T A 2105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 U 4 G U 2004 1_555 C N6 A 5 T A 2105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog6 B N6 A 5 G A 2005 1_555 C O2 U 4 T U 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog7 B O2 C 6 G C 2006 1_555 C N1 G 3 T G 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog8 B O2 C 7 G C 2007 1_555 C N1 G 2 T G 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 C 8 G C 2008 1_555 C N1 G 1 T G 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 C 8 G C 2008 1_555 C O6 G 1 T G 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 C 8 G C 2008 1_555 C N2 G 1 T G 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 3VNU _atom_sites.fract_transf_matrix[1][1] 0.007194 _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] 0.003914 _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] 0.00986 _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 D 4 ATP A 1 2501 2501 ATP ATP . E 5 CA A 1 2502 3001 CA CA . F 5 CA A 1 2503 3002 CA CA . G 6 HOH A 1 3101 3101 HOH HOH . G 6 HOH A 2 3102 3102 HOH HOH . G 6 HOH A 3 3103 3103 HOH HOH . G 6 HOH A 4 3104 3104 HOH HOH . G 6 HOH A 5 3105 3105 HOH HOH . G 6 HOH A 6 3106 3106 HOH HOH . G 6 HOH A 7 3107 3107 HOH HOH . G 6 HOH A 8 3108 3108 HOH HOH . G 6 HOH A 9 3109 3109 HOH HOH . G 6 HOH A 10 3110 3111 HOH HOH . G 6 HOH A 11 3111 3110 HOH HOH . H 6 HOH T 1 2201 3112 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 F _atom_site.label_entity_id 5 _atom_site.Cartn_x 19.526 _atom_site.Cartn_y 66.43 _atom_site.Cartn_z -6.921 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 33.95 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 2503 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #