data_6J26 # _model_server_result.job_id MG4DWgBRPLiBPlVisyZl2A _model_server_result.datetime_utc '2024-11-12 21:41:28' _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 6j26 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 6J26 # _exptl.entry_id 6J26 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 264.474 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N~1~,N~1~,N~1~-tris(3-azaniumylpropyl)butane-1,4-diaminium _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 120 _cell.entry_id 6J26 _cell.length_a 74.17 _cell.length_b 74.17 _cell.length_c 105.934 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6J26 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G 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 SG CYS 111 A CYS 91 1_555 E FE FE . A FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc2 A SG CYS 114 A CYS 94 1_555 E FE FE . A FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc3 E FE FE . A FE 403 1_555 B SG CYS 111 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc4 E FE FE . A FE 403 1_555 B SG CYS 114 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? # _chem_comp.formula 'C13 H38 N5 5' _chem_comp.formula_weight 264.474 _chem_comp.id B5L _chem_comp.mon_nstd_flag . _chem_comp.name N~1~,N~1~,N~1~-tris(3-azaniumylpropyl)butane-1,4-diaminium _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N4-bis(aminopropyl)spermidine # 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 N14 C13 B5L sing 70 n n C2 C3 B5L sing 71 n n C2 N1 B5L sing 72 n n C3 C4 B5L sing 73 n n C13 C12 B5L sing 74 n n C12 C11 B5L sing 75 n n C4 C5 B5L sing 76 n n C5 N6 B5L sing 77 n n C8 C7 B5L sing 78 n n C8 C9 B5L sing 79 n n C7 N6 B5L sing 80 n n C9 N10 B5L sing 81 n n C11 N6 B5L sing 82 n n N6 C15 B5L sing 83 n n C15 C16 B5L sing 84 n n C16 C17 B5L sing 85 n n C17 N18 B5L sing 86 n n C5 H1 B5L sing 87 n n C5 H2 B5L sing 88 n n C4 H3 B5L sing 89 n n C4 H4 B5L sing 90 n n C3 H5 B5L sing 91 n n C3 H6 B5L sing 92 n n C2 H7 B5L sing 93 n n C2 H8 B5L sing 94 n n N18 H9 B5L sing 95 n n N18 H10 B5L sing 96 n n N18 H11 B5L sing 97 n n C17 H12 B5L sing 98 n n C17 H13 B5L sing 99 n n C16 H14 B5L sing 100 n n C16 H15 B5L sing 101 n n C15 H16 B5L sing 102 n n C15 H17 B5L sing 103 n n C11 H18 B5L sing 104 n n C11 H19 B5L sing 105 n n C12 H20 B5L sing 106 n n C12 H21 B5L sing 107 n n C13 H22 B5L sing 108 n n C13 H23 B5L sing 109 n n N14 H24 B5L sing 110 n n N14 H25 B5L sing 111 n n N14 H26 B5L sing 112 n n C7 H27 B5L sing 113 n n C7 H28 B5L sing 114 n n C8 H29 B5L sing 115 n n C8 H30 B5L sing 116 n n C9 H31 B5L sing 117 n n C9 H32 B5L sing 118 n n N10 H33 B5L sing 119 n n N10 H34 B5L sing 120 n n N10 H35 B5L sing 121 n n N1 H36 B5L sing 122 n n N1 H37 B5L sing 123 n n N1 H38 B5L sing 124 n n # _atom_sites.entry_id 6J26 _atom_sites.fract_transf_matrix[1][1] 0.013483 _atom_sites.fract_transf_matrix[1][2] 0.007784 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015568 _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] 0.00944 _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 MTA A 1 401 1000 MTA MTA . D 3 B5L A 1 402 2 B5L 44S . E 4 FE A 1 403 1 FE FE . F 2 MTA B 1 401 1000 MTA MTA . G 3 B5L B 1 402 1 B5L 44S . H 5 HOH A 1 501 108 HOH HOH . H 5 HOH A 2 502 96 HOH HOH . H 5 HOH A 3 503 181 HOH HOH . H 5 HOH A 4 504 97 HOH HOH . H 5 HOH A 5 505 111 HOH HOH . H 5 HOH A 6 506 144 HOH HOH . H 5 HOH A 7 507 38 HOH HOH . H 5 HOH A 8 508 9 HOH HOH . H 5 HOH A 9 509 205 HOH HOH . H 5 HOH A 10 510 150 HOH HOH . H 5 HOH A 11 511 60 HOH HOH . H 5 HOH A 12 512 29 HOH HOH . H 5 HOH A 13 513 124 HOH HOH . H 5 HOH A 14 514 129 HOH HOH . H 5 HOH A 15 515 66 HOH HOH . H 5 HOH A 16 516 116 HOH HOH . H 5 HOH A 17 517 112 HOH HOH . H 5 HOH A 18 518 23 HOH HOH . H 5 HOH A 19 519 222 HOH HOH . H 5 HOH A 20 520 74 HOH HOH . H 5 HOH A 21 521 226 HOH HOH . H 5 HOH A 22 522 36 HOH HOH . H 5 HOH A 23 523 103 HOH HOH . H 5 HOH A 24 524 15 HOH HOH . H 5 HOH A 25 525 40 HOH HOH . H 5 HOH A 26 526 18 HOH HOH . H 5 HOH A 27 527 125 HOH HOH . H 5 HOH A 28 528 122 HOH HOH . H 5 HOH A 29 529 1 HOH HOH . H 5 HOH A 30 530 137 HOH HOH . H 5 HOH A 31 531 75 HOH HOH . H 5 HOH A 32 532 199 HOH HOH . H 5 HOH A 33 533 201 HOH HOH . H 5 HOH A 34 534 69 HOH HOH . H 5 HOH A 35 535 43 HOH HOH . H 5 HOH A 36 536 26 HOH HOH . H 5 HOH A 37 537 77 HOH HOH . H 5 HOH A 38 538 215 HOH HOH . H 5 HOH A 39 539 152 HOH HOH . H 5 HOH A 40 540 27 HOH HOH . H 5 HOH A 41 541 143 HOH HOH . H 5 HOH A 42 542 33 HOH HOH . H 5 HOH A 43 543 31 HOH HOH . H 5 HOH A 44 544 219 HOH HOH . H 5 HOH A 45 545 151 HOH HOH . H 5 HOH A 46 546 51 HOH HOH . H 5 HOH A 47 547 223 HOH HOH . H 5 HOH A 48 548 227 HOH HOH . H 5 HOH A 49 549 149 HOH HOH . H 5 HOH A 50 550 4 HOH HOH . H 5 HOH A 51 551 230 HOH HOH . H 5 HOH A 52 552 70 HOH HOH . H 5 HOH A 53 553 214 HOH HOH . H 5 HOH A 54 554 228 HOH HOH . H 5 HOH A 55 555 61 HOH HOH . H 5 HOH A 56 556 64 HOH HOH . H 5 HOH A 57 557 212 HOH HOH . H 5 HOH A 58 558 209 HOH HOH . H 5 HOH A 59 559 188 HOH HOH . H 5 HOH A 60 560 48 HOH HOH . H 5 HOH A 61 561 213 HOH HOH . H 5 HOH A 62 562 224 HOH HOH . H 5 HOH A 63 563 140 HOH HOH . H 5 HOH A 64 564 21 HOH HOH . H 5 HOH A 65 565 7 HOH HOH . H 5 HOH A 66 566 5 HOH HOH . H 5 HOH A 67 567 184 HOH HOH . H 5 HOH A 68 568 105 HOH HOH . H 5 HOH A 69 569 203 HOH HOH . H 5 HOH A 70 570 221 HOH HOH . H 5 HOH A 71 571 135 HOH HOH . H 5 HOH A 72 572 211 HOH HOH . H 5 HOH A 73 573 155 HOH HOH . H 5 HOH A 74 574 83 HOH HOH . H 5 HOH A 75 575 208 HOH HOH . H 5 HOH A 76 576 50 HOH HOH . H 5 HOH A 77 577 258 HOH HOH . H 5 HOH A 78 578 47 HOH HOH . H 5 HOH A 79 579 110 HOH HOH . H 5 HOH A 80 580 68 HOH HOH . H 5 HOH A 81 581 180 HOH HOH . H 5 HOH A 82 582 34 HOH HOH . H 5 HOH A 83 583 82 HOH HOH . H 5 HOH A 84 584 55 HOH HOH . H 5 HOH A 85 585 133 HOH HOH . H 5 HOH A 86 586 16 HOH HOH . H 5 HOH A 87 587 218 HOH HOH . H 5 HOH A 88 588 206 HOH HOH . H 5 HOH A 89 589 210 HOH HOH . H 5 HOH A 90 590 179 HOH HOH . H 5 HOH A 91 591 52 HOH HOH . H 5 HOH A 92 592 234 HOH HOH . H 5 HOH A 93 593 202 HOH HOH . H 5 HOH A 94 594 196 HOH HOH . H 5 HOH A 95 595 197 HOH HOH . H 5 HOH A 96 596 204 HOH HOH . I 5 HOH B 1 501 156 HOH HOH . I 5 HOH B 2 502 239 HOH HOH . I 5 HOH B 3 503 81 HOH HOH . I 5 HOH B 4 504 217 HOH HOH . I 5 HOH B 5 505 248 HOH HOH . I 5 HOH B 6 506 2 HOH HOH . I 5 HOH B 7 507 207 HOH HOH . I 5 HOH B 8 508 113 HOH HOH . I 5 HOH B 9 509 65 HOH HOH . I 5 HOH B 10 510 240 HOH HOH . I 5 HOH B 11 511 146 HOH HOH . I 5 HOH B 12 512 41 HOH HOH . I 5 HOH B 13 513 225 HOH HOH . I 5 HOH B 14 514 138 HOH HOH . I 5 HOH B 15 515 256 HOH HOH . I 5 HOH B 16 516 131 HOH HOH . I 5 HOH B 17 517 243 HOH HOH . I 5 HOH B 18 518 91 HOH HOH . I 5 HOH B 19 519 44 HOH HOH . I 5 HOH B 20 520 92 HOH HOH . I 5 HOH B 21 521 245 HOH HOH . I 5 HOH B 22 522 85 HOH HOH . I 5 HOH B 23 523 101 HOH HOH . I 5 HOH B 24 524 72 HOH HOH . I 5 HOH B 25 525 229 HOH HOH . I 5 HOH B 26 526 99 HOH HOH . I 5 HOH B 27 527 53 HOH HOH . I 5 HOH B 28 528 30 HOH HOH . I 5 HOH B 29 529 35 HOH HOH . I 5 HOH B 30 530 67 HOH HOH . I 5 HOH B 31 531 236 HOH HOH . I 5 HOH B 32 532 42 HOH HOH . I 5 HOH B 33 533 59 HOH HOH . I 5 HOH B 34 534 193 HOH HOH . I 5 HOH B 35 535 166 HOH HOH . I 5 HOH B 36 536 252 HOH HOH . I 5 HOH B 37 537 136 HOH HOH . I 5 HOH B 38 538 57 HOH HOH . I 5 HOH B 39 539 79 HOH HOH . I 5 HOH B 40 540 22 HOH HOH . I 5 HOH B 41 541 28 HOH HOH . I 5 HOH B 42 542 173 HOH HOH . I 5 HOH B 43 543 175 HOH HOH . I 5 HOH B 44 544 78 HOH HOH . I 5 HOH B 45 545 14 HOH HOH . I 5 HOH B 46 546 45 HOH HOH . I 5 HOH B 47 547 159 HOH HOH . I 5 HOH B 48 548 98 HOH HOH . I 5 HOH B 49 549 10 HOH HOH . I 5 HOH B 50 550 154 HOH HOH . I 5 HOH B 51 551 109 HOH HOH . I 5 HOH B 52 552 246 HOH HOH . I 5 HOH B 53 553 259 HOH HOH . I 5 HOH B 54 554 153 HOH HOH . I 5 HOH B 55 555 6 HOH HOH . I 5 HOH B 56 556 25 HOH HOH . I 5 HOH B 57 557 123 HOH HOH . I 5 HOH B 58 558 100 HOH HOH . I 5 HOH B 59 559 46 HOH HOH . I 5 HOH B 60 560 145 HOH HOH . I 5 HOH B 61 561 3 HOH HOH . I 5 HOH B 62 562 141 HOH HOH . I 5 HOH B 63 563 107 HOH HOH . I 5 HOH B 64 564 71 HOH HOH . I 5 HOH B 65 565 238 HOH HOH . I 5 HOH B 66 566 62 HOH HOH . I 5 HOH B 67 567 187 HOH HOH . I 5 HOH B 68 568 242 HOH HOH . I 5 HOH B 69 569 39 HOH HOH . I 5 HOH B 70 570 93 HOH HOH . I 5 HOH B 71 571 237 HOH HOH . I 5 HOH B 72 572 37 HOH HOH . I 5 HOH B 73 573 250 HOH HOH . I 5 HOH B 74 574 102 HOH HOH . I 5 HOH B 75 575 104 HOH HOH . I 5 HOH B 76 576 94 HOH HOH . I 5 HOH B 77 577 63 HOH HOH . I 5 HOH B 78 578 54 HOH HOH . I 5 HOH B 79 579 249 HOH HOH . I 5 HOH B 80 580 87 HOH HOH . I 5 HOH B 81 581 176 HOH HOH . I 5 HOH B 82 582 186 HOH HOH . I 5 HOH B 83 583 119 HOH HOH . I 5 HOH B 84 584 216 HOH HOH . I 5 HOH B 85 585 19 HOH HOH . I 5 HOH B 86 586 232 HOH HOH . I 5 HOH B 87 587 95 HOH HOH . I 5 HOH B 88 588 49 HOH HOH . I 5 HOH B 89 589 220 HOH HOH . I 5 HOH B 90 590 235 HOH HOH . I 5 HOH B 91 591 255 HOH HOH . I 5 HOH B 92 592 241 HOH HOH . I 5 HOH B 93 593 257 HOH HOH . I 5 HOH B 94 594 174 HOH HOH . I 5 HOH B 95 595 247 HOH HOH . I 5 HOH B 96 596 244 HOH HOH . I 5 HOH B 97 597 128 HOH HOH . I 5 HOH B 98 598 233 HOH HOH . I 5 HOH B 99 599 148 HOH HOH . I 5 HOH B 100 600 254 HOH HOH . I 5 HOH B 101 601 142 HOH HOH . I 5 HOH B 102 602 200 HOH HOH . I 5 HOH B 103 603 198 HOH HOH . I 5 HOH B 104 604 80 HOH HOH . I 5 HOH B 105 605 231 HOH HOH . I 5 HOH B 106 606 253 HOH HOH . I 5 HOH B 107 607 251 HOH HOH . I 5 HOH B 108 608 84 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 C C5 B5L . . . G 3 74.299 69.368 16.631 1 30.74 ? C5 B5L 402 B 1 HETATM 2 C C4 B5L . . . G 3 75.506 70.318 16.547 1 30.44 ? C4 B5L 402 B 1 HETATM 3 C C3 B5L . . . G 3 76.689 69.705 15.815 1 30.4 ? C3 B5L 402 B 1 HETATM 4 C C2 B5L . . . G 3 77.863 70.682 15.812 1 30.36 ? C2 B5L 402 B 1 HETATM 5 N N18 B5L . . . G 3 76.323 68.518 20.738 1 33.08 ? N18 B5L 402 B 1 HETATM 6 C C17 B5L . . . G 3 75.705 67.982 19.519 1 32.9 ? C17 B5L 402 B 1 HETATM 7 C C16 B5L . . . G 3 74.202 68.196 19.495 1 32.23 ? C16 B5L 402 B 1 HETATM 8 C C15 B5L . . . G 3 73.776 69.592 19.03 1 31.57 ? C15 B5L 402 B 1 HETATM 9 N N6 B5L . . . G 3 73.257 69.754 17.632 1 31.09 ? N6 B5L 402 B 1 HETATM 10 C C11 B5L . . . G 3 72.903 71.203 17.539 1 30.77 ? C11 B5L 402 B 1 HETATM 11 C C12 B5L . . . G 3 72.554 71.747 16.144 1 30.81 ? C12 B5L 402 B 1 HETATM 12 C C13 B5L . . . G 3 71.294 72.595 16.138 1 31.1 ? C13 B5L 402 B 1 HETATM 13 N N14 B5L . . . G 3 70.705 72.621 14.794 1 31.36 ? N14 B5L 402 B 1 HETATM 14 C C7 B5L . . . G 3 71.956 69.024 17.468 1 30.99 ? C7 B5L 402 B 1 HETATM 15 C C8 B5L . . . G 3 71.97 67.555 17.019 1 30.81 ? C8 B5L 402 B 1 HETATM 16 C C9 B5L . . . G 3 70.737 66.79 17.512 1 30.78 ? C9 B5L 402 B 1 HETATM 17 N N10 B5L . . . G 3 70.488 66.976 18.951 1 30.44 ? N10 B5L 402 B 1 HETATM 18 N N1 B5L . . . G 3 78.381 70.911 17.172 1 29.99 ? N1 B5L 402 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 18 #