data_6BQ7 # _model_server_result.job_id NEfN_f2ZCntBnXDUG3uSfw _model_server_result.datetime_utc '2024-11-16 13:02:52' _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 6bq7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 6BQ7 # _exptl.entry_id 6BQ7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 2 _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 90 _cell.angle_gamma 90 _cell.entry_id 6BQ7 _cell.length_a 79.962 _cell.length_b 79.962 _cell.length_c 163.532 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BQ7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _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 290 n n N1 HN11 SPD sing 291 n n N1 HN12 SPD sing 292 n n C2 C3 SPD sing 293 n n C2 H21 SPD sing 294 n n C2 H22 SPD sing 295 n n C3 C4 SPD sing 296 n n C3 H31 SPD sing 297 n n C3 H32 SPD sing 298 n n C4 C5 SPD sing 299 n n C4 H41 SPD sing 300 n n C4 H42 SPD sing 301 n n C5 N6 SPD sing 302 n n C5 H51 SPD sing 303 n n C5 H52 SPD sing 304 n n N6 C7 SPD sing 305 n n N6 HN6 SPD sing 306 n n C7 C8 SPD sing 307 n n C7 H71 SPD sing 308 n n C7 H72 SPD sing 309 n n C8 C9 SPD sing 310 n n C8 H81 SPD sing 311 n n C8 H82 SPD sing 312 n n C9 N10 SPD sing 313 n n C9 H91 SPD sing 314 n n C9 H92 SPD sing 315 n n N10 H101 SPD sing 316 n n N10 H102 SPD sing 317 n n # _atom_sites.entry_id 6BQ7 _atom_sites.fract_transf_matrix[1][1] 0.012506 _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] 0.012506 _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] 0.006115 _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 C 2 SPD A 1 401 2 SPD SPD . D 2 SPD B 1 401 1 SPD SPD . E 3 HOH A 1 501 69 HOH HOH . E 3 HOH A 2 502 6 HOH HOH . E 3 HOH A 3 503 17 HOH HOH . E 3 HOH A 4 504 95 HOH HOH . E 3 HOH A 5 505 80 HOH HOH . E 3 HOH A 6 506 81 HOH HOH . E 3 HOH A 7 507 7 HOH HOH . E 3 HOH A 8 508 16 HOH HOH . E 3 HOH A 9 509 19 HOH HOH . E 3 HOH A 10 510 62 HOH HOH . E 3 HOH A 11 511 73 HOH HOH . E 3 HOH A 12 512 25 HOH HOH . E 3 HOH A 13 513 110 HOH HOH . E 3 HOH A 14 514 76 HOH HOH . E 3 HOH A 15 515 43 HOH HOH . E 3 HOH A 16 516 65 HOH HOH . E 3 HOH A 17 517 28 HOH HOH . E 3 HOH A 18 518 61 HOH HOH . E 3 HOH A 19 519 33 HOH HOH . E 3 HOH A 20 520 72 HOH HOH . E 3 HOH A 21 521 35 HOH HOH . E 3 HOH A 22 522 38 HOH HOH . E 3 HOH A 23 523 58 HOH HOH . E 3 HOH A 24 524 66 HOH HOH . E 3 HOH A 25 525 59 HOH HOH . E 3 HOH A 26 526 75 HOH HOH . E 3 HOH A 27 527 57 HOH HOH . E 3 HOH A 28 528 42 HOH HOH . E 3 HOH A 29 529 79 HOH HOH . E 3 HOH A 30 530 53 HOH HOH . E 3 HOH A 31 531 99 HOH HOH . E 3 HOH A 32 532 34 HOH HOH . E 3 HOH A 33 533 50 HOH HOH . E 3 HOH A 34 534 108 HOH HOH . E 3 HOH A 35 535 107 HOH HOH . E 3 HOH A 36 536 83 HOH HOH . E 3 HOH A 37 537 44 HOH HOH . E 3 HOH A 38 538 15 HOH HOH . E 3 HOH A 39 539 26 HOH HOH . E 3 HOH A 40 540 24 HOH HOH . E 3 HOH A 41 541 60 HOH HOH . E 3 HOH A 42 542 89 HOH HOH . E 3 HOH A 43 543 90 HOH HOH . E 3 HOH A 44 544 67 HOH HOH . E 3 HOH A 45 545 105 HOH HOH . E 3 HOH A 46 546 3 HOH HOH . E 3 HOH A 47 547 98 HOH HOH . E 3 HOH A 48 548 1 HOH HOH . E 3 HOH A 49 549 93 HOH HOH . E 3 HOH A 50 550 30 HOH HOH . E 3 HOH A 51 551 94 HOH HOH . E 3 HOH A 52 552 36 HOH HOH . E 3 HOH A 53 553 55 HOH HOH . E 3 HOH A 54 554 5 HOH HOH . E 3 HOH A 55 555 102 HOH HOH . E 3 HOH A 56 556 86 HOH HOH . E 3 HOH A 57 557 64 HOH HOH . E 3 HOH A 58 558 111 HOH HOH . E 3 HOH A 59 559 96 HOH HOH . E 3 HOH A 60 560 112 HOH HOH . E 3 HOH A 61 561 54 HOH HOH . E 3 HOH A 62 562 78 HOH HOH . E 3 HOH A 63 563 103 HOH HOH . E 3 HOH A 64 564 31 HOH HOH . E 3 HOH A 65 565 87 HOH HOH . E 3 HOH A 66 566 77 HOH HOH . E 3 HOH A 67 567 106 HOH HOH . E 3 HOH A 68 568 104 HOH HOH . E 3 HOH A 69 569 91 HOH HOH . F 3 HOH B 1 501 97 HOH HOH . F 3 HOH B 2 502 22 HOH HOH . F 3 HOH B 3 503 84 HOH HOH . F 3 HOH B 4 504 101 HOH HOH . F 3 HOH B 5 505 11 HOH HOH . F 3 HOH B 6 506 2 HOH HOH . F 3 HOH B 7 507 29 HOH HOH . F 3 HOH B 8 508 68 HOH HOH . F 3 HOH B 9 509 49 HOH HOH . F 3 HOH B 10 510 40 HOH HOH . F 3 HOH B 11 511 63 HOH HOH . F 3 HOH B 12 512 12 HOH HOH . F 3 HOH B 13 513 51 HOH HOH . F 3 HOH B 14 514 113 HOH HOH . F 3 HOH B 15 515 52 HOH HOH . F 3 HOH B 16 516 47 HOH HOH . F 3 HOH B 17 517 21 HOH HOH . F 3 HOH B 18 518 85 HOH HOH . F 3 HOH B 19 519 46 HOH HOH . F 3 HOH B 20 520 71 HOH HOH . F 3 HOH B 21 521 100 HOH HOH . F 3 HOH B 22 522 14 HOH HOH . F 3 HOH B 23 523 8 HOH HOH . F 3 HOH B 24 524 109 HOH HOH . F 3 HOH B 25 525 20 HOH HOH . F 3 HOH B 26 526 41 HOH HOH . F 3 HOH B 27 527 10 HOH HOH . F 3 HOH B 28 528 32 HOH HOH . F 3 HOH B 29 529 88 HOH HOH . F 3 HOH B 30 530 27 HOH HOH . F 3 HOH B 31 531 56 HOH HOH . F 3 HOH B 32 532 37 HOH HOH . F 3 HOH B 33 533 70 HOH HOH . F 3 HOH B 34 534 39 HOH HOH . F 3 HOH B 35 535 13 HOH HOH . F 3 HOH B 36 536 18 HOH HOH . F 3 HOH B 37 537 4 HOH HOH . F 3 HOH B 38 538 9 HOH HOH . F 3 HOH B 39 539 48 HOH HOH . F 3 HOH B 40 540 92 HOH HOH . F 3 HOH B 41 541 82 HOH HOH . F 3 HOH B 42 542 23 HOH HOH . F 3 HOH B 43 543 74 HOH HOH . F 3 HOH B 44 544 45 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 . . . D 2 21.167 27.309 15.266 1 64.86 ? N1 SPD 401 B 1 HETATM 2 C C2 SPD . . . D 2 21.014 26.881 16.655 1 66.39 ? C2 SPD 401 B 1 HETATM 3 C C3 SPD . . . D 2 21.943 27.677 17.564 1 60.39 ? C3 SPD 401 B 1 HETATM 4 C C4 SPD . . . D 2 21.441 29.103 17.726 1 54.55 ? C4 SPD 401 B 1 HETATM 5 C C5 SPD . . . D 2 20.839 29.248 19.126 1 53.61 ? C5 SPD 401 B 1 HETATM 6 N N6 SPD . . . D 2 21.365 30.47 19.713 1 59.71 ? N6 SPD 401 B 1 HETATM 7 C C7 SPD . . . D 2 20.847 30.681 21.061 1 64.22 ? C7 SPD 401 B 1 HETATM 8 C C8 SPD . . . D 2 21.105 32.134 21.466 1 65.41 ? C8 SPD 401 B 1 HETATM 9 C C9 SPD . . . D 2 19.762 32.848 21.614 1 70.48 ? C9 SPD 401 B 1 HETATM 10 N N10 SPD . . . D 2 19.976 34.281 21.714 1 75.51 ? N10 SPD 401 B 1 # _model_server_stats.io_time_ms 87 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #