data_1MYP # _model_server_result.job_id NOioikOF8uUlndF3-e5skA _model_server_result.datetime_utc '2025-04-12 10:03:20' _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 1myp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":201}' # _entry.id 1MYP # _exptl.entry_id 1MYP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 4 _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 1MYP _cell.length_a 133 _cell.length_b 133 _cell.length_c 203.6 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MYP _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J,K,L,M,N _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 ? 4 K N N ? 4 M N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 NAG _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 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 3 n E NAG 1 E 1 NAG A 582 NAG 3 n E NAG 2 E 2 NAG A 583 NAG 3 n F NAG 1 F 1 NAG A 584 NAG 3 n F NAG 2 F 2 NAG A 585 NAG 3 n G NAG 1 G 1 NAG A 586 NAG 3 n G NAG 2 G 2 NAG A 587 NAG 3 n H NAG 1 H 1 NAG B 582 NAG 3 n H NAG 2 H 2 NAG B 583 NAG 3 n I NAG 1 I 1 NAG B 584 NAG 3 n I NAG 2 I 2 NAG B 585 NAG 3 n J NAG 1 J 1 NAG B 586 NAG 3 n J NAG 2 J 2 NAG B 587 NAG # 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 3 A CYS 1 1_555 A SG CYS 16 A CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 B SG CYS 3 C CYS 115 1_555 B SG CYS 13 C CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 B SG CYS 7 C CYS 119 1_555 B SG CYS 31 C CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf4 B SG CYS 41 C CYS 153 1_555 D SG CYS 41 D CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf5 B SG CYS 109 C CYS 221 1_555 B SG CYS 120 C CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 328 C CYS 440 1_555 B SG CYS 385 C CYS 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf7 B SG CYS 426 C CYS 538 1_555 B SG CYS 452 C CYS 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 C SG CYS 3 B CYS 1 1_555 C SG CYS 16 B CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 D SG CYS 3 D CYS 115 1_555 D SG CYS 13 D CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 D SG CYS 7 D CYS 119 1_555 D SG CYS 31 D CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf11 D SG CYS 109 D CYS 221 1_555 D SG CYS 120 D CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf12 D SG CYS 328 D CYS 440 1_555 D SG CYS 385 D CYS 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf13 D SG CYS 426 D CYS 538 1_555 D SG CYS 452 D CYS 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 B ND2 ASN 77 C ASN 189 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale2 B ND2 ASN 113 C ASN 225 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale3 B ND2 ASN 205 C ASN 317 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale4 D ND2 ASN 77 D ASN 189 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 D ND2 ASN 113 D ASN 225 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 D ND2 ASN 205 D ASN 317 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale10 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale11 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale12 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.365 ? metalc ? metalc1 A O ASP 98 A ASP 96 1_555 K CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc2 A OD1 ASP 98 A ASP 96 1_555 K CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.639 ? metalc ? metalc3 K CA CA . A CA 201 1_555 B OG1 THR 56 C THR 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc4 K CA CA . A CA 201 1_555 B O THR 56 C THR 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc5 K CA CA . A CA 201 1_555 B O PHE 58 C PHE 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc6 K CA CA . A CA 201 1_555 B OD1 ASP 60 C ASP 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc7 K CA CA . A CA 201 1_555 B OG SER 62 C SER 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc8 B NE2 HIS 224 C HIS 336 1_555 L FE HEM . C HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc9 C OD1 ASP 98 B ASP 96 1_555 M CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc10 C O ASP 98 B ASP 96 1_555 M CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc11 D OG1 THR 56 D THR 168 1_555 M CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc12 D O THR 56 D THR 168 1_555 M CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc13 D O PHE 58 D PHE 170 1_555 M CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc14 D OD1 ASP 60 D ASP 172 1_555 M CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc15 D OG SER 62 D SER 174 1_555 M CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc16 D NE2 HIS 224 D HIS 336 1_555 N FE HEM . D HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? # _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 1MYP _atom_sites.fract_transf_matrix[1][1] 0.007519 _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] 0.007519 _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] 0.004912 _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 K 4 CA A 1 201 581 CA CA . L 5 HEM C 1 601 580 HEM HEM . M 4 CA D 1 601 581 CA CA . N 5 HEM D 1 602 580 HEM HEM . # _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 K _atom_site.label_entity_id 4 _atom_site.Cartn_x 49.424 _atom_site.Cartn_y 60.98 _atom_site.Cartn_z 26.494 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 15 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 201 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #