data_8E6N # _model_server_result.job_id kJmhui5FaPlyCbw2Uoa_vg _model_server_result.datetime_utc '2025-03-03 03:13:13' _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 8e6n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":525}' # _entry.id 8E6N # _exptl.entry_id 8E6N _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.72 _cell.angle_gamma 90 _cell.entry_id 8E6N _cell.length_a 105.758 _cell.length_b 80.389 _cell.length_c 51.754 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E6N _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 ? 5 Z N N ? 5 AA N 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 metalc ? metalc1 A O ALA 28 A ALA 53 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc2 A OD1 ASP 31 A ASP 56 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc3 A NE2 HIS 262 A HIS 287 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc4 A NE2 HIS 262 A HIS 287 1_555 C MN MN . A MN 502 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc5 B MN MN . A MN 501 1_555 BA O HOH . A HOH 625 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc6 B MN MN . A MN 501 1_555 BA O HOH . A HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc7 C MN MN . A MN 502 1_555 BA O HOH . A HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc8 C MN MN . A MN 502 1_555 BA O HOH . A HOH 620 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? # _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 370 n n N1 HN11 SPD sing 371 n n N1 HN12 SPD sing 372 n n C2 C3 SPD sing 373 n n C2 H21 SPD sing 374 n n C2 H22 SPD sing 375 n n C3 C4 SPD sing 376 n n C3 H31 SPD sing 377 n n C3 H32 SPD sing 378 n n C4 C5 SPD sing 379 n n C4 H41 SPD sing 380 n n C4 H42 SPD sing 381 n n C5 N6 SPD sing 382 n n C5 H51 SPD sing 383 n n C5 H52 SPD sing 384 n n N6 C7 SPD sing 385 n n N6 HN6 SPD sing 386 n n C7 C8 SPD sing 387 n n C7 H71 SPD sing 388 n n C7 H72 SPD sing 389 n n C8 C9 SPD sing 390 n n C8 H81 SPD sing 391 n n C8 H82 SPD sing 392 n n C9 N10 SPD sing 393 n n C9 H91 SPD sing 394 n n C9 H92 SPD sing 395 n n N10 H101 SPD sing 396 n n N10 H102 SPD sing 397 n n # _atom_sites.entry_id 8E6N _atom_sites.fract_transf_matrix[1][1] 0.009456 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000781 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01244 _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] 0.019388 _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 MN A 1 501 501 MN MN . C 2 MN A 1 502 502 MN MN . D 3 OLC A 1 503 503 OLC OLC . E 3 OLC A 1 504 504 OLC OLC . F 3 OLC A 1 505 505 OLC OLC . G 3 OLC A 1 506 506 OLC OLC . H 3 OLC A 1 507 507 OLC OLC . I 3 OLC A 1 508 508 OLC OLC . J 3 OLC A 1 509 509 OLC OLC . K 3 OLC A 1 510 510 OLC OLC . L 3 OLC A 1 511 511 OLC OLC . M 3 OLC A 1 512 512 OLC OLC . N 3 OLC A 1 513 513 OLC OLC . O 3 OLC A 1 514 514 OLC OLC . P 3 OLC A 1 515 515 OLC OLC . Q 3 OLC A 1 516 516 OLC OLC . R 3 OLC A 1 517 517 OLC OLC . S 3 OLC A 1 518 518 OLC OLC . T 3 OLC A 1 519 519 OLC OLC . U 3 OLC A 1 520 520 OLC OLC . V 4 PEG A 1 521 521 PEG PEG . W 4 PEG A 1 522 522 PEG PEG . X 4 PEG A 1 523 523 PEG PEG . Y 4 PEG A 1 524 524 PEG PEG . Z 5 SPD A 1 525 525 SPD SPD . AA 5 SPD A 1 526 526 SPD SPD . BA 6 HOH A 1 601 614 HOH HOH . BA 6 HOH A 2 602 601 HOH HOH . BA 6 HOH A 3 603 603 HOH HOH . BA 6 HOH A 4 604 602 HOH HOH . BA 6 HOH A 5 605 653 HOH HOH . BA 6 HOH A 6 606 604 HOH HOH . BA 6 HOH A 7 607 611 HOH HOH . BA 6 HOH A 8 608 605 HOH HOH . BA 6 HOH A 9 609 607 HOH HOH . BA 6 HOH A 10 610 609 HOH HOH . BA 6 HOH A 11 611 650 HOH HOH . BA 6 HOH A 12 612 608 HOH HOH . BA 6 HOH A 13 613 606 HOH HOH . BA 6 HOH A 14 614 613 HOH HOH . BA 6 HOH A 15 615 620 HOH HOH . BA 6 HOH A 16 616 629 HOH HOH . BA 6 HOH A 17 617 615 HOH HOH . BA 6 HOH A 18 618 621 HOH HOH . BA 6 HOH A 19 619 612 HOH HOH . BA 6 HOH A 20 620 624 HOH HOH . BA 6 HOH A 21 621 625 HOH HOH . BA 6 HOH A 22 622 610 HOH HOH . BA 6 HOH A 23 623 640 HOH HOH . BA 6 HOH A 24 624 616 HOH HOH . BA 6 HOH A 25 625 652 HOH HOH . BA 6 HOH A 26 626 617 HOH HOH . BA 6 HOH A 27 627 631 HOH HOH . BA 6 HOH A 28 628 618 HOH HOH . BA 6 HOH A 29 629 630 HOH HOH . BA 6 HOH A 30 630 627 HOH HOH . BA 6 HOH A 31 631 651 HOH HOH . BA 6 HOH A 32 632 619 HOH HOH . BA 6 HOH A 33 633 623 HOH HOH . BA 6 HOH A 34 634 628 HOH HOH . BA 6 HOH A 35 635 636 HOH HOH . BA 6 HOH A 36 636 626 HOH HOH . BA 6 HOH A 37 637 634 HOH HOH . BA 6 HOH A 38 638 633 HOH HOH . BA 6 HOH A 39 639 635 HOH HOH . BA 6 HOH A 40 640 622 HOH HOH . BA 6 HOH A 41 641 637 HOH HOH . BA 6 HOH A 42 642 632 HOH HOH . BA 6 HOH A 43 643 639 HOH HOH . BA 6 HOH A 44 644 638 HOH HOH . BA 6 HOH A 45 645 644 HOH HOH . BA 6 HOH A 46 646 641 HOH HOH . BA 6 HOH A 47 647 642 HOH HOH . BA 6 HOH A 48 648 643 HOH HOH . BA 6 HOH A 49 649 649 HOH HOH . BA 6 HOH A 50 650 645 HOH HOH . BA 6 HOH A 51 651 646 HOH HOH . BA 6 HOH A 52 652 647 HOH HOH . BA 6 HOH A 53 653 654 HOH HOH . BA 6 HOH A 54 654 648 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 . . . Z 5 -47.165 -43.358 16.5 1 110.5 ? N1 SPD 525 A 1 HETATM 2 C C2 SPD . . . Z 5 -46.549 -42.489 15.513 1 103.49 ? C2 SPD 525 A 1 HETATM 3 C C3 SPD . . . Z 5 -45.082 -42.268 15.872 1 110.19 ? C3 SPD 525 A 1 HETATM 4 C C4 SPD . . . Z 5 -44.415 -43.615 16.137 1 101.04 ? C4 SPD 525 A 1 HETATM 5 C C5 SPD . . . Z 5 -42.897 -43.461 16.069 1 108.85 ? C5 SPD 525 A 1 HETATM 6 N N6 SPD . . . Z 5 -42.419 -43.914 14.774 1 102.63 ? N6 SPD 525 A 1 HETATM 7 C C7 SPD . . . Z 5 -41.436 -42.973 14.268 1 109.51 ? C7 SPD 525 A 1 HETATM 8 C C8 SPD . . . Z 5 -42.151 -41.732 13.738 1 105.74 ? C8 SPD 525 A 1 HETATM 9 C C9 SPD . . . Z 5 -41.119 -40.701 13.289 1 98.81 ? C9 SPD 525 A 1 HETATM 10 N N10 SPD . . . Z 5 -40.196 -41.321 12.356 1 84.86 ? N10 SPD 525 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #