data_9FYO # _model_server_result.job_id vZOuofjGyRFUPHPbvuIAVA _model_server_result.datetime_utc '2024-10-09 23:22:26' _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 9fyo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1103}' # _entry.id 9FYO # _exptl.entry_id 9FYO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) 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 90 _cell.entry_id 9FYO _cell.length_a 90.759 _cell.length_b 93.686 _cell.length_c 94.037 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9FYO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 3 C N N ? 3 D N N ? 3 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n B NAG 1 C 1 NAG C 1 NAG 2 n B GAL 2 C 2 GAL C 2 GAL # 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 A SG CYS 151 A CYS 423 1_555 A SG CYS 153 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 547 A CYS 819 1_555 A SG CYS 572 A CYS 844 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 B O3 NAG . C NAG 1 1_555 B C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? metalc ? metalc1 A NE2 HIS 20 A HIS 292 1_555 E NI NI . A NI 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc2 A NE2 HIS 225 A HIS 497 1_555 C NI NI . A NI 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc3 A NE2 HIS 535 A HIS 807 1_555 D NI NI . A NI 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc4 D NI NI . A NI 1102 1_555 F O HOH . A HOH 1217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc5 D NI NI . A NI 1102 1_555 F O HOH . A HOH 1221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc6 E NI NI . A NI 1103 1_555 F O HOH . A HOH 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc7 E NI NI . A NI 1103 1_555 F O HOH . A HOH 1214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc8 E NI NI . A NI 1103 1_555 F O HOH . A HOH 1223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 9FYO _atom_sites.fract_transf_matrix[1][1] 0.011018 _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] 0.010674 _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] 0.010634 _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 C 3 NI A 1 1101 2 NI NI . D 3 NI A 1 1102 3 NI NI . E 3 NI A 1 1103 4 NI NI . F 4 HOH A 1 1201 20 HOH HOH . F 4 HOH A 2 1202 19 HOH HOH . F 4 HOH A 3 1203 24 HOH HOH . F 4 HOH A 4 1204 7 HOH HOH . F 4 HOH A 5 1205 4 HOH HOH . F 4 HOH A 6 1206 12 HOH HOH . F 4 HOH A 7 1207 10 HOH HOH . F 4 HOH A 8 1208 11 HOH HOH . F 4 HOH A 9 1209 1 HOH HOH . F 4 HOH A 10 1210 17 HOH HOH . F 4 HOH A 11 1211 9 HOH HOH . F 4 HOH A 12 1212 13 HOH HOH . F 4 HOH A 13 1213 18 HOH HOH . F 4 HOH A 14 1214 22 HOH HOH . F 4 HOH A 15 1215 15 HOH HOH . F 4 HOH A 16 1216 8 HOH HOH . F 4 HOH A 17 1217 3 HOH HOH . F 4 HOH A 18 1218 5 HOH HOH . F 4 HOH A 19 1219 21 HOH HOH . F 4 HOH A 20 1220 6 HOH HOH . F 4 HOH A 21 1221 2 HOH HOH . F 4 HOH A 22 1222 16 HOH HOH . F 4 HOH A 23 1223 23 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 3 _atom_site.Cartn_x 9.807 _atom_site.Cartn_y 23.433 _atom_site.Cartn_z -23.28 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 128.47 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 1103 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #