data_3F9P # _model_server_result.job_id rIEeNKvLHuqd7EUNuSdIRw _model_server_result.datetime_utc '2024-10-18 15:24:49' _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 3f9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":601}' # _entry.id 3F9P # _exptl.entry_id 3F9P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 6 _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 3F9P _cell.length_a 110.74 _cell.length_b 110.74 _cell.length_c 255.333 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3F9P _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H,I,J,K,L 1 1 C,D,F,M,N,O,P,Q,R 2 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 ? 6 I N N ? 6 N N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 BMA BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 BMA BMA C1 O1 . O6 HO6 . sing 5 ? 3 6 1 FUC NAG C1 O1 . O6 HO6 . 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 640 NAG 3 n E NAG 2 E 2 NAG A 641 NAG 3 n E BMA 3 E 3 BMA A 642 BMA 3 n E BMA 4 E 4 BMA A 643 BMA 3 n E BMA 5 E 5 BMA A 644 BMA 3 n E FUC 6 E 6 FUC A 645 FUC 3 n F NAG 1 F 1 NAG B 640 NAG 3 n F NAG 2 F 2 NAG B 641 NAG 3 n F BMA 3 F 3 BMA B 642 BMA 3 n F BMA 4 F 4 BMA B 643 BMA 3 n F BMA 5 F 5 BMA B 644 BMA 3 n F FUC 6 F 6 FUC B 645 FUC # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 3 C CYS 115 1_555 B SG CYS 13 C CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 7 C CYS 119 1_555 B SG CYS 31 C CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 41 C CYS 153 1_555 D SG CYS 41 D CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 109 C CYS 221 1_555 B SG CYS 120 C CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 328 C CYS 440 1_555 B SG CYS 385 C CYS 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 426 C CYS 538 1_555 B SG CYS 452 C CYS 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 C SG CYS 3 B CYS 1 1_555 C SG CYS 16 B CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 D SG CYS 3 D CYS 115 1_555 D SG CYS 13 D CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 D SG CYS 7 D CYS 119 1_555 D SG CYS 31 D CYS 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 D SG CYS 109 D CYS 221 1_555 D SG CYS 120 D CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 D SG CYS 328 D CYS 440 1_555 D SG CYS 385 D CYS 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf13 D SG CYS 426 D CYS 538 1_555 D SG CYS 452 D CYS 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A OD1 ASP 96 A ASP 94 1_555 H CMD HEM . A HEM 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 H CMB HEM . A HEM 605 1_555 B OE2 GLU 130 C GLU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 H CBB HEM . A HEM 605 1_555 B SD MET 131 C MET 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? covale ? covale4 B C SER 37 C SER 149 1_555 B N CSO 38 C CSO 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 B C CSO 38 C CSO 150 1_555 B N PRO 39 C PRO 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale6 B ND2 ASN 77 C ASN 189 1_555 J C1 NAG . C NAG 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 B ND2 ASN 113 C ASN 225 1_555 K C1 NAG . C NAG 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 B ND2 ASN 205 C ASN 317 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale9 C OD1 ASP 96 B ASP 94 1_555 M CMD HEM . B HEM 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 M CMB HEM . B HEM 605 1_555 D OE2 GLU 130 D GLU 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale11 M CBB HEM . B HEM 605 1_555 D SD MET 131 D MET 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale12 D C SER 37 D SER 149 1_555 D N CSO 38 D CSO 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 D C CSO 38 D CSO 150 1_555 D N PRO 39 D PRO 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale14 D ND2 ASN 77 D ASN 189 1_555 P C1 NAG . D NAG 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale15 D ND2 ASN 113 D ASN 225 1_555 Q C1 NAG . D NAG 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 D ND2 ASN 205 D ASN 317 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale17 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale19 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale20 E O3 BMA . E BMA 3 1_555 E C1 BMA . E BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale21 E O6 BMA . E BMA 3 1_555 E C1 BMA . E BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale22 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale23 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale24 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale25 F O3 BMA . F BMA 3 1_555 F C1 BMA . F BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale26 F O6 BMA . F BMA 3 1_555 F C1 BMA . F BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? metalc ? metalc1 A O ASP 98 A ASP 96 1_555 I CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc2 A OD2 ASP 98 A ASP 96 1_555 I CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc3 H FE HEM . A HEM 605 1_555 B NE2 HIS 224 C HIS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc4 B O THR 56 C THR 168 1_555 I CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc5 B OG1 THR 56 C THR 168 1_555 I CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc6 B O PHE 58 C PHE 170 1_555 I CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc7 B OD1 ASP 60 C ASP 172 1_555 I CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc8 B OG SER 62 C SER 174 1_555 I CA CA . C CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc9 C O ASP 98 B ASP 96 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc10 C OD2 ASP 98 B ASP 96 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc11 M FE HEM . B HEM 605 1_555 D NE2 HIS 224 D HIS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc12 D O THR 56 D THR 168 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc13 D OG1 THR 56 D THR 168 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc14 D O PHE 58 D PHE 170 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc15 D OD1 ASP 60 D ASP 172 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc16 D OG SER 62 D SER 174 1_555 N CA CA . D CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? # _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 3F9P _atom_sites.fract_transf_matrix[1][1] 0.00903 _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] 0.00903 _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] 0.003916 _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 4 CL A 1 602 602 CL CL . H 5 HEM A 1 605 605 HEM HEM . I 6 CA C 1 601 601 CA CA . J 7 NAG C 1 620 620 NAG NAG . K 7 NAG C 1 630 630 NAG NAG . L 8 ACT C 1 703 703 ACT ACT . M 5 HEM B 1 605 605 HEM HEM . N 6 CA D 1 601 601 CA CA . O 4 CL D 1 602 602 CL CL . P 7 NAG D 1 620 620 NAG NAG . Q 7 NAG D 1 630 630 NAG NAG . R 8 ACT D 1 703 703 ACT ACT . # _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 N _atom_site.label_entity_id 6 _atom_site.Cartn_x -7.402 _atom_site.Cartn_y -4.496 _atom_site.Cartn_z -29.549 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 67.11 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 601 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #