data_5VYG # _model_server_result.job_id RaqM5lVsiTQLUxMp2MyvUQ _model_server_result.datetime_utc '2025-08-31 18:04:31' _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 5vyg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":103}' # _entry.id 5VYG # _exptl.entry_id 5VYG _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.58 _cell.angle_gamma 90 _cell.entry_id 5VYG _cell.length_a 92.417 _cell.length_b 46.84 _cell.length_c 37.259 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VYG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G,H,J 1 1 B,E,K 2 1 C,F,I,L 3 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 G N N ? 3 H N N ? 3 I 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 XYS BGC C1 O1 . O3 HO3 . sing 2 ? 2 3 2 XYS XYS C1 O1 . O3 HO3 . 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 D BGC 1 D 1 BGC D 2 GXX 2 n D XYS 2 D 2 XYS D 2 GXX 2 n D XYS 3 D 3 XYS D 2 GXX 2 n E BGC 1 E 1 BGC D 1 GXX 2 n E XYS 2 E 2 XYS D 1 GXX 2 n E XYS 3 E 3 XYS D 1 GXX 2 n F BGC 1 F 1 BGC D 3 GXX 2 n F XYS 2 F 2 XYS D 3 GXX 2 n F XYS 3 F 3 XYS D 3 GXX # 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 9 B CYS 51 1_555 A SG CYS 20 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 A SG CYS 14 B CYS 56 1_555 A SG CYS 29 B CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 31 B CYS 73 1_555 A SG CYS 40 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf4 B SG CYS 9 A CYS 51 1_555 B SG CYS 20 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf5 B SG CYS 14 A CYS 56 1_555 B SG CYS 29 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 31 A CYS 73 1_555 B SG CYS 40 A CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf7 C SG CYS 9 C CYS 51 1_555 C SG CYS 20 C CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf8 C SG CYS 14 C CYS 56 1_555 C SG CYS 29 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 C SG CYS 31 C CYS 73 1_555 C SG CYS 40 C CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? covale ? covale1 A OG SER 11 B SER 53 1_555 D C1 BGC . D BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.207 ? covale ? covale2 B OG SER 11 A SER 53 1_555 E C1 BGC . E BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale3 C OG SER 11 C SER 53 1_555 F C1 BGC . F BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? covale ? covale4 D O3 BGC . D BGC 1 1_555 D C1 XYS . D XYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 sing covale ? covale5 D O3 XYS . D XYS 2 1_555 D C1 XYS . D XYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 sing covale ? covale6 E O3 BGC . E BGC 1 1_555 E C1 XYS . E XYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 sing covale ? covale7 E O3 XYS . E XYS 2 1_555 E C1 XYS . E XYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 sing covale ? covale8 F O3 BGC . F BGC 1 1_555 F C1 XYS . F XYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 sing covale ? covale9 F O3 XYS . F XYS 2 1_555 F C1 XYS . F XYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 sing metalc ? metalc1 A OD2 ASP 5 B ASP 47 1_555 G CA CA . B CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc2 A O GLY 6 B GLY 48 1_555 G CA CA . B CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc3 A OE1 GLN 8 B GLN 50 1_555 G CA CA . B CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc4 A OD1 ASN 16 B ASN 58 1_555 H CA CA . B CA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc5 A OD1 ASP 22 B ASP 64 1_555 G CA CA . B CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc6 A OD2 ASP 22 B ASP 64 1_555 G CA CA . B CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc7 A O ASP 23 B ASP 65 1_555 G CA CA . B CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc8 G CA CA . B CA 102 1_555 C OD1 ASN 16 C ASN 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc9 H CA CA . B CA 103 1_555 B OD1 ASP 5 A ASP 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc10 H CA CA . B CA 103 1_555 B O GLY 6 A GLY 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc11 H CA CA . B CA 103 1_555 B OE1 GLN 8 A GLN 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc12 H CA CA . B CA 103 1_555 B OD1 ASP 22 A ASP 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc13 H CA CA . B CA 103 1_555 B OD2 ASP 22 A ASP 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc14 H CA CA . B CA 103 1_555 B O ASP 23 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc15 B OD1 ASN 16 A ASN 58 1_555 I CA CA . C CA 102 1_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc16 C OD2 ASP 5 C ASP 47 1_555 I CA CA . C CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? metalc ? metalc17 C O GLY 6 C GLY 48 1_555 I CA CA . C CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc18 C OE1 GLN 8 C GLN 50 1_555 I CA CA . C CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc19 C OD1 ASP 22 C ASP 64 1_555 I CA CA . C CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc20 C OD2 ASP 22 C ASP 64 1_555 I CA CA . C CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc21 C O ASP 23 C ASP 65 1_555 I CA CA . C CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? # _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 5VYG _atom_sites.fract_transf_matrix[1][1] 0.01082 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000487 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021349 _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] 0.026867 _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 3 CA B 1 102 1 CA CA . H 3 CA B 1 103 3 CA CA . I 3 CA C 1 102 2 CA CA . J 4 HOH B 1 201 33 HOH HOH . J 4 HOH B 2 202 9 HOH HOH . J 4 HOH B 3 203 36 HOH HOH . J 4 HOH B 4 204 34 HOH HOH . J 4 HOH B 5 205 21 HOH HOH . J 4 HOH B 6 206 2 HOH HOH . J 4 HOH B 7 207 12 HOH HOH . J 4 HOH B 8 208 31 HOH HOH . J 4 HOH B 9 209 1 HOH HOH . J 4 HOH B 10 210 39 HOH HOH . K 4 HOH A 1 201 22 HOH HOH . K 4 HOH A 2 202 17 HOH HOH . K 4 HOH A 3 203 28 HOH HOH . K 4 HOH A 4 204 37 HOH HOH . K 4 HOH A 5 205 35 HOH HOH . K 4 HOH A 6 206 32 HOH HOH . K 4 HOH A 7 207 23 HOH HOH . K 4 HOH A 8 208 20 HOH HOH . K 4 HOH A 9 209 15 HOH HOH . K 4 HOH A 10 210 40 HOH HOH . K 4 HOH A 11 211 7 HOH HOH . K 4 HOH A 12 212 11 HOH HOH . L 4 HOH C 1 201 26 HOH HOH . L 4 HOH C 2 202 14 HOH HOH . L 4 HOH C 3 203 16 HOH HOH . L 4 HOH C 4 204 30 HOH HOH . L 4 HOH C 5 205 19 HOH HOH . L 4 HOH C 6 206 18 HOH HOH . L 4 HOH C 7 207 6 HOH HOH . L 4 HOH C 8 208 10 HOH HOH . L 4 HOH C 9 209 8 HOH HOH . L 4 HOH C 10 210 24 HOH HOH . L 4 HOH C 11 211 13 HOH HOH . L 4 HOH C 12 212 5 HOH HOH . L 4 HOH C 13 213 27 HOH HOH . L 4 HOH C 14 214 38 HOH HOH . L 4 HOH C 15 215 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 H _atom_site.label_entity_id 3 _atom_site.Cartn_x -11.136 _atom_site.Cartn_y 9.131 _atom_site.Cartn_z 16.32 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 28.41 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 103 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 4 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 392 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #