data_5VYB # _model_server_result.job_id OC2d3RQ-3RDun7t-MtTymg _model_server_result.datetime_utc '2025-02-05 05:56:56' _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 5vyb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":309}' # _entry.id 5VYB # _exptl.entry_id 5VYB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 3 _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 5VYB _cell.length_a 64.055 _cell.length_b 78.834 _cell.length_c 76.459 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VYB _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 MAN BMA C1 O1 . O3 HO3 . sing 2 ? 2 3 2 MAN MAN C1 O1 . O2 HO2 . sing 3 ? 2 4 3 MAN MAN C1 O1 . O2 HO2 . sing 4 ? 2 5 1 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 2 6 5 MAN MAN C1 O1 . O3 HO3 . sing 6 ? 2 7 6 MAN MAN C1 O1 . O2 HO2 . 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 BMA 1 B 1 BMA A 303 BMA 2 n B MAN 2 B 2 MAN A 302 MAN 2 n B MAN 3 B 3 MAN A 301 MAN 2 n B MAN 4 B 4 MAN A 300 MAN 2 n B MAN 5 B 5 MAN A 304 MAN 2 n B MAN 6 B 6 MAN A 305 MAN 2 n B MAN 7 B 7 MAN A 306 MAN # 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 4 A CYS 66 1_555 A SG CYS 16 A CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 17 A CYS 79 1_555 A SG CYS 28 A CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 45 A CYS 107 1_555 A SG CYS 140 A CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 A SG CYS 114 A CYS 176 1_555 A SG CYS 132 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 B O3 BMA . B BMA 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 B O6 BMA . B BMA 1 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 B O2 MAN . B MAN 2 1_555 B C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B O2 MAN . B MAN 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B O3 MAN . B MAN 5 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B O2 MAN . B MAN 6 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 A O VAL 54 A VAL 116 1_555 D CA CA . A CA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc2 A OD1 ASN 56 A ASN 118 1_555 D CA CA . A CA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc3 A OE1 GLU 60 A GLU 122 1_555 D CA CA . A CA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc4 A OE2 GLU 60 A GLU 122 1_555 D CA CA . A CA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc5 A OE1 GLU 106 A GLU 168 1_555 C CA CA . A CA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc6 A OD1 ASN 108 A ASN 170 1_555 C CA CA . A CA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc7 A O HIS 109 A HIS 171 1_555 E NA NA . A NA 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc8 A OE1 GLU 112 A GLU 174 1_555 C CA CA . A CA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc9 A O GLU 112 A GLU 174 1_555 E NA NA . A NA 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc10 A OD1 ASN 128 A ASN 190 1_555 C CA CA . A CA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc11 A O ASP 129 A ASP 191 1_555 C CA CA . A CA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc12 A OD1 ASP 129 A ASP 191 1_555 C CA CA . A CA 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc13 A OD2 ASP 129 A ASP 191 1_555 E NA NA . A NA 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc14 A OE1 GLU 141 A GLU 203 1_555 D CA CA . A CA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc15 A OE2 GLU 141 A GLU 203 1_555 D CA CA . A CA 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.004 ? metalc ? metalc16 C CA CA . A CA 308 1_555 B O3 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc17 C CA CA . A CA 308 1_555 B O4 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc18 C CA CA . A CA 308 4_566 B O3 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc19 C CA CA . A CA 308 4_566 B O4 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc20 D CA CA . A CA 309 1_555 G O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc21 D CA CA . A CA 309 1_555 G O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc22 E NA NA . A NA 310 1_555 G O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc23 E NA NA . A NA 310 1_555 G O HOH . A HOH 412 8_456 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? # _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 5VYB _atom_sites.fract_transf_matrix[1][1] 0.015611 _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] 0.012685 _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] 0.013079 _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 CA A 1 308 400 CA CA . D 3 CA A 1 309 401 CA CA . E 4 NA A 1 310 402 NA NA . F 5 PEG A 1 311 1 PEG PEG . G 6 HOH A 1 401 18 HOH HOH . G 6 HOH A 2 402 3 HOH HOH . G 6 HOH A 3 403 16 HOH HOH . G 6 HOH A 4 404 5 HOH HOH . G 6 HOH A 5 405 6 HOH HOH . G 6 HOH A 6 406 17 HOH HOH . G 6 HOH A 7 407 8 HOH HOH . G 6 HOH A 8 408 1 HOH HOH . G 6 HOH A 9 409 19 HOH HOH . G 6 HOH A 10 410 9 HOH HOH . G 6 HOH A 11 411 7 HOH HOH . G 6 HOH A 12 412 4 HOH HOH . G 6 HOH A 13 413 10 HOH HOH . G 6 HOH A 14 414 2 HOH HOH . G 6 HOH A 15 415 11 HOH HOH . G 6 HOH A 16 416 12 HOH HOH . G 6 HOH A 17 417 15 HOH HOH . G 6 HOH A 18 418 13 HOH HOH . G 6 HOH A 19 419 14 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 D _atom_site.label_entity_id 3 _atom_site.Cartn_x 43.816 _atom_site.Cartn_y 14.115 _atom_site.Cartn_z 50.485 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 46.98 _atom_site.pdbx_formal_charge 2 _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 309 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 378 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #