data_4OGC # _model_server_result.job_id lTQKHKH8fThl9tZ-huIz2A _model_server_result.datetime_utc '2024-11-28 09:13:49' _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 4ogc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1205}' # _entry.id 4OGC # _exptl.entry_id 4OGC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.38 _cell.angle_gamma 90 _cell.entry_id 4OGC _cell.length_a 74.61 _cell.length_b 132.56 _cell.length_c 80.04 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OGC _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 covale ? covale1 A C ILE 365 A ILE 365 1_555 A N MSE 366 A MSE 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 366 A MSE 366 1_555 A N ARG 367 A ARG 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale3 A C ALA 388 A ALA 388 1_555 A N MSE 389 A MSE 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 389 A MSE 389 1_555 A N ILE 390 A ILE 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C HIS 440 A HIS 440 1_555 A N MSE 441 A MSE 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C MSE 441 A MSE 441 1_555 A N LEU 442 A LEU 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A C SER 494 A SER 494 1_555 A N MSE 495 A MSE 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 A C MSE 495 A MSE 495 1_555 A N TRP 496 A TRP 496 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 A C ARG 515 A ARG 515 1_555 A N MSE 516 A MSE 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 A C MSE 516 A MSE 516 1_555 A N ALA 517 A ALA 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale11 A C ALA 534 A ALA 534 1_555 A N MSE 535 A MSE 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale12 A C MSE 535 A MSE 535 1_555 A N LYS 536 A LYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 A C SER 674 A SER 674 1_555 A N MSE 675 A MSE 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale14 A C MSE 675 A MSE 675 1_555 A N GLU 676 A GLU 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale15 A C TRP 680 A TRP 680 1_555 A N MSE 681 A MSE 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale16 A C MSE 681 A MSE 681 1_555 A N ALA 682 A ALA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale17 A C VAL 698 A VAL 698 1_555 A N MSE 699 A MSE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale18 A C MSE 699 A MSE 699 1_555 A N VAL 700 A VAL 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale19 A C LEU 745 A LEU 745 1_555 A N MSE 746 A MSE 746 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale20 A C MSE 746 A MSE 746 1_555 A N GLU 747 A GLU 747 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale21 A C GLU 788 A GLU 788 1_555 A N MSE 789 A MSE 789 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale22 A C MSE 789 A MSE 789 1_555 A N TRP 790 A TRP 790 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale23 A C HIS 793 A HIS 793 1_555 A N MSE 794 A MSE 794 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale24 A C MSE 794 A MSE 794 1_555 A N LEU 795 A LEU 795 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale25 A C ALA 942 A ALA 942 1_555 A N MSE 943 A MSE 943 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale26 A C MSE 943 A MSE 943 1_555 A N LEU 944 A LEU 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale27 A C SER 970 A SER 970 1_555 A N MSE 971 A MSE 971 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale28 A C MSE 971 A MSE 971 1_555 A N ARG 972 A ARG 972 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD2 ASP 17 A ASP 17 1_555 C MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc2 A OD1 ASP 17 A ASP 17 1_555 G MN MN . A MN 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc3 A OE1 GLU 505 A GLU 505 1_555 G MN MN . A MN 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc4 A SG CYS 566 A CYS 566 1_555 B ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc5 A SG CYS 569 A CYS 569 1_555 B ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc6 A OD1 ASP 581 A ASP 581 1_555 E MG MG . A MG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc7 A O GLN 586 A GLN 586 1_555 D MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc8 A O GLY 588 A GLY 588 1_555 D MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc9 A O GLY 590 A GLY 590 1_555 D MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc10 A SG CYS 602 A CYS 602 1_555 B ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc11 A SG CYS 605 A CYS 605 1_555 B ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc12 A OD1 ASN 606 A ASN 606 1_555 E MG MG . A MG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc13 A ND1 HIS 736 A HIS 736 1_555 C MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc14 C MN MN . A MN 1202 1_555 I O HOH . A HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc15 D MG MG . A MG 1203 1_555 I O HOH . A HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc16 D MG MG . A MG 1203 1_555 I O HOH . A HOH 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc17 D MG MG . A MG 1203 1_555 I O HOH . A HOH 1309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc18 E MG MG . A MG 1204 1_555 I O HOH . A HOH 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc19 E MG MG . A MG 1204 1_555 I O HOH . A HOH 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc20 E MG MG . A MG 1204 1_555 I O HOH . A HOH 1306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc21 E MG MG . A MG 1204 1_555 I O HOH . A HOH 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 SPD sing 296 n n N1 HN11 SPD sing 297 n n N1 HN12 SPD sing 298 n n C2 C3 SPD sing 299 n n C2 H21 SPD sing 300 n n C2 H22 SPD sing 301 n n C3 C4 SPD sing 302 n n C3 H31 SPD sing 303 n n C3 H32 SPD sing 304 n n C4 C5 SPD sing 305 n n C4 H41 SPD sing 306 n n C4 H42 SPD sing 307 n n C5 N6 SPD sing 308 n n C5 H51 SPD sing 309 n n C5 H52 SPD sing 310 n n N6 C7 SPD sing 311 n n N6 HN6 SPD sing 312 n n C7 C8 SPD sing 313 n n C7 H71 SPD sing 314 n n C7 H72 SPD sing 315 n n C8 C9 SPD sing 316 n n C8 H81 SPD sing 317 n n C8 H82 SPD sing 318 n n C9 N10 SPD sing 319 n n C9 H91 SPD sing 320 n n C9 H92 SPD sing 321 n n N10 H101 SPD sing 322 n n N10 H102 SPD sing 323 n n # _atom_sites.entry_id 4OGC _atom_sites.fract_transf_matrix[1][1] 0.013403 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001262 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007544 _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] 0.012549 _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 B 2 ZN A 1 1201 1 ZN ZN . C 3 MN A 1 1202 2 MN MN . D 4 MG A 1 1203 3 MG MG . E 4 MG A 1 1204 4 MG MG . F 5 SPD A 1 1205 5 SPD SPD . G 3 MN A 1 1206 6 MN MN . H 6 ACT A 1 1207 7 ACT ACT . I 7 HOH A 1 1301 1 HOH HOH . I 7 HOH A 2 1302 2 HOH HOH . I 7 HOH A 3 1303 3 HOH HOH . I 7 HOH A 4 1304 4 HOH HOH . I 7 HOH A 5 1305 5 HOH HOH . I 7 HOH A 6 1306 6 HOH HOH . I 7 HOH A 7 1307 7 HOH HOH . I 7 HOH A 8 1308 8 HOH HOH . I 7 HOH A 9 1309 9 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 SPD . . . F 5 18.784 49.107 -3.064 1 89.89 ? N1 SPD 1205 A 1 HETATM 2 C C2 SPD . . . F 5 19.157 47.777 -3.466 1 95.32 ? C2 SPD 1205 A 1 HETATM 3 C C3 SPD . . . F 5 20.01 47.849 -4.734 1 97.91 ? C3 SPD 1205 A 1 HETATM 4 C C4 SPD . . . F 5 20.215 46.461 -5.362 1 93.1 ? C4 SPD 1205 A 1 HETATM 5 C C5 SPD . . . F 5 21.111 46.579 -6.612 1 86.26 ? C5 SPD 1205 A 1 HETATM 6 N N6 SPD . . . F 5 21.217 45.291 -7.275 1 78.64 ? N6 SPD 1205 A 1 HETATM 7 C C7 SPD . . . F 5 22.533 45.093 -7.848 1 68.18 ? C7 SPD 1205 A 1 HETATM 8 C C8 SPD . . . F 5 23.198 43.879 -7.188 1 62.56 ? C8 SPD 1205 A 1 HETATM 9 C C9 SPD . . . F 5 23.878 43.018 -8.253 1 65.29 ? C9 SPD 1205 A 1 HETATM 10 N N10 SPD . . . F 5 24.464 41.843 -7.662 1 66.35 ? N10 SPD 1205 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 367 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 10 #