data_6VJ6 # _model_server_result.job_id fJXNTUCXH_Gu-wtRVpa68g _model_server_result.datetime_utc '2024-11-09 02:45:52' _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 6vj6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 6VJ6 # _exptl.entry_id 6VJ6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 279.373 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,6,9,12,15-pentaoxaoctadecan-17-amine _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 91.749 _cell.angle_gamma 90 _cell.entry_id 6VJ6 _cell.length_a 151.425 _cell.length_b 70.358 _cell.length_c 79.357 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VJ6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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,C,D,E,G 1 1,2 B,F,H 2 1,3 # 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' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -2.42206 0 79.320029 3 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 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 F 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 covale ? covale1 A C GLU 34 A GLU 56 1_555 A N MSE 35 A MSE 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C MSE 35 A MSE 57 1_555 A N VAL 36 A VAL 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale3 A C LYS 62 A LYS 84 1_555 A N MSE 63 A MSE 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A C MSE 63 A MSE 85 1_555 A N GLY 64 A GLY 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale5 A C TYR 70 A TYR 92 1_555 A N MSE 71 A MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale6 A C MSE 71 A MSE 93 1_555 A N GLU 72 A GLU 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale7 A C GLY 165 A GLY 187 1_555 A N MSE 166 A MSE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale8 A C MSE 166 A MSE 188 1_555 A N MSE 167 A MSE 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale9 A C MSE 167 A MSE 189 1_555 A N VAL 168 A VAL 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale10 B C GLU 34 B GLU 56 1_555 B N MSE 35 B MSE 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale11 B C MSE 35 B MSE 57 1_555 B N VAL 36 B VAL 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale12 B C LYS 62 B LYS 84 1_555 B N MSE 63 B MSE 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale13 B C MSE 63 B MSE 85 1_555 B N GLY 64 B GLY 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale14 B C TYR 70 B TYR 92 1_555 B N MSE 71 B MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale15 B C MSE 71 B MSE 93 1_555 B N GLU 72 B GLU 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale16 B C GLY 165 B GLY 187 1_555 B N MSE 166 B MSE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale17 B C MSE 166 B MSE 188 1_555 B N MSE 167 B MSE 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale18 B C MSE 167 B MSE 189 1_555 B N VAL 168 B VAL 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? # _chem_comp.formula 'C13 H29 N O5' _chem_comp.formula_weight 279.373 _chem_comp.id 2NV _chem_comp.mon_nstd_flag . _chem_comp.name 3,6,9,12,15-pentaoxaoctadecan-17-amine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Jeffamine ED-2001' # 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 2NV sing 1 n n N1 HN1 2NV sing 2 n n N1 HN1A 2NV sing 3 n n C3 C2 2NV sing 4 n n C2 C2A 2NV sing 5 n n C2 H2 2NV sing 6 n n O4 C3 2NV sing 7 n n C3 H3 2NV sing 8 n n C3 H3A 2NV sing 9 n n C5 O4 2NV sing 10 n n C5 C6 2NV sing 11 n n C5 H5 2NV sing 12 n n C5 H5A 2NV sing 13 n n O7 C6 2NV sing 14 n n C6 H6 2NV sing 15 n n C6 H6A 2NV sing 16 n n O7 C8 2NV sing 17 n n C8 C9 2NV sing 18 n n C8 H8 2NV sing 19 n n C8 H8A 2NV sing 20 n n O10 C9 2NV sing 21 n n C9 H9 2NV sing 22 n n C9 H9A 2NV sing 23 n n O10 C11 2NV sing 24 n n C11 C12 2NV sing 25 n n C11 H11 2NV sing 26 n n C11 H11A 2NV sing 27 n n C12 O13 2NV sing 28 n n C12 H12 2NV sing 29 n n C12 H12A 2NV sing 30 n n O13 C14 2NV sing 31 n n C14 C15 2NV sing 32 n n C14 H14 2NV sing 33 n n C14 H14A 2NV sing 34 n n C15 O16 2NV sing 35 n n C15 H15 2NV sing 36 n n C15 H15A 2NV sing 37 n n O16 C17 2NV sing 38 n n C17 C18 2NV sing 39 n n C17 H17 2NV sing 40 n n C17 H17A 2NV sing 41 n n C18 H18 2NV sing 42 n n C18 H18A 2NV sing 43 n n C18 H18B 2NV sing 44 n n C2A H2A 2NV sing 45 n n C2A H2AA 2NV sing 46 n n C2A H2AB 2NV sing 47 n n # _atom_sites.entry_id 6VJ6 _atom_sites.fract_transf_matrix[1][1] 0.006604 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000202 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014213 _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] 0.012607 _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 2NV A 1 301 1 2NV 2NV . D 3 GOL A 1 302 3 GOL GOL . E 3 GOL A 1 303 4 GOL GOL . F 2 2NV B 1 301 2 2NV 2NV . G 4 HOH A 1 401 46 HOH HOH . G 4 HOH A 2 402 99 HOH HOH . G 4 HOH A 3 403 15 HOH HOH . G 4 HOH A 4 404 115 HOH HOH . G 4 HOH A 5 405 5 HOH HOH . G 4 HOH A 6 406 108 HOH HOH . G 4 HOH A 7 407 10 HOH HOH . G 4 HOH A 8 408 37 HOH HOH . G 4 HOH A 9 409 42 HOH HOH . G 4 HOH A 10 410 21 HOH HOH . G 4 HOH A 11 411 136 HOH HOH . G 4 HOH A 12 412 51 HOH HOH . G 4 HOH A 13 413 9 HOH HOH . G 4 HOH A 14 414 64 HOH HOH . G 4 HOH A 15 415 58 HOH HOH . G 4 HOH A 16 416 48 HOH HOH . G 4 HOH A 17 417 45 HOH HOH . G 4 HOH A 18 418 20 HOH HOH . G 4 HOH A 19 419 103 HOH HOH . G 4 HOH A 20 420 98 HOH HOH . G 4 HOH A 21 421 72 HOH HOH . G 4 HOH A 22 422 47 HOH HOH . G 4 HOH A 23 423 85 HOH HOH . G 4 HOH A 24 424 84 HOH HOH . G 4 HOH A 25 425 25 HOH HOH . G 4 HOH A 26 426 39 HOH HOH . G 4 HOH A 27 427 101 HOH HOH . G 4 HOH A 28 428 142 HOH HOH . G 4 HOH A 29 429 141 HOH HOH . G 4 HOH A 30 430 49 HOH HOH . G 4 HOH A 31 431 56 HOH HOH . G 4 HOH A 32 432 79 HOH HOH . G 4 HOH A 33 433 75 HOH HOH . G 4 HOH A 34 434 130 HOH HOH . G 4 HOH A 35 435 94 HOH HOH . G 4 HOH A 36 436 120 HOH HOH . G 4 HOH A 37 437 36 HOH HOH . G 4 HOH A 38 438 34 HOH HOH . G 4 HOH A 39 439 12 HOH HOH . G 4 HOH A 40 440 134 HOH HOH . G 4 HOH A 41 441 22 HOH HOH . G 4 HOH A 42 442 19 HOH HOH . G 4 HOH A 43 443 125 HOH HOH . G 4 HOH A 44 444 66 HOH HOH . G 4 HOH A 45 445 41 HOH HOH . G 4 HOH A 46 446 40 HOH HOH . G 4 HOH A 47 447 11 HOH HOH . G 4 HOH A 48 448 87 HOH HOH . G 4 HOH A 49 449 71 HOH HOH . G 4 HOH A 50 450 159 HOH HOH . G 4 HOH A 51 451 104 HOH HOH . G 4 HOH A 52 452 17 HOH HOH . G 4 HOH A 53 453 18 HOH HOH . G 4 HOH A 54 454 97 HOH HOH . G 4 HOH A 55 455 77 HOH HOH . G 4 HOH A 56 456 53 HOH HOH . G 4 HOH A 57 457 33 HOH HOH . G 4 HOH A 58 458 38 HOH HOH . G 4 HOH A 59 459 135 HOH HOH . G 4 HOH A 60 460 57 HOH HOH . G 4 HOH A 61 461 122 HOH HOH . G 4 HOH A 62 462 143 HOH HOH . G 4 HOH A 63 463 63 HOH HOH . G 4 HOH A 64 464 91 HOH HOH . G 4 HOH A 65 465 96 HOH HOH . G 4 HOH A 66 466 83 HOH HOH . G 4 HOH A 67 467 132 HOH HOH . G 4 HOH A 68 468 116 HOH HOH . G 4 HOH A 69 469 59 HOH HOH . G 4 HOH A 70 470 100 HOH HOH . G 4 HOH A 71 471 23 HOH HOH . G 4 HOH A 72 472 117 HOH HOH . G 4 HOH A 73 473 124 HOH HOH . G 4 HOH A 74 474 93 HOH HOH . G 4 HOH A 75 475 127 HOH HOH . G 4 HOH A 76 476 73 HOH HOH . G 4 HOH A 77 477 88 HOH HOH . G 4 HOH A 78 478 89 HOH HOH . G 4 HOH A 79 479 128 HOH HOH . G 4 HOH A 80 480 112 HOH HOH . G 4 HOH A 81 481 44 HOH HOH . G 4 HOH A 82 482 106 HOH HOH . G 4 HOH A 83 483 133 HOH HOH . G 4 HOH A 84 484 123 HOH HOH . G 4 HOH A 85 485 111 HOH HOH . G 4 HOH A 86 486 109 HOH HOH . G 4 HOH A 87 487 157 HOH HOH . H 4 HOH B 1 401 70 HOH HOH . H 4 HOH B 2 402 31 HOH HOH . H 4 HOH B 3 403 8 HOH HOH . H 4 HOH B 4 404 102 HOH HOH . H 4 HOH B 5 405 158 HOH HOH . H 4 HOH B 6 406 67 HOH HOH . H 4 HOH B 7 407 7 HOH HOH . H 4 HOH B 8 408 82 HOH HOH . H 4 HOH B 9 409 27 HOH HOH . H 4 HOH B 10 410 6 HOH HOH . H 4 HOH B 11 411 145 HOH HOH . H 4 HOH B 12 412 160 HOH HOH . H 4 HOH B 13 413 137 HOH HOH . H 4 HOH B 14 414 50 HOH HOH . H 4 HOH B 15 415 69 HOH HOH . H 4 HOH B 16 416 52 HOH HOH . H 4 HOH B 17 417 90 HOH HOH . H 4 HOH B 18 418 138 HOH HOH . H 4 HOH B 19 419 28 HOH HOH . H 4 HOH B 20 420 78 HOH HOH . H 4 HOH B 21 421 16 HOH HOH . H 4 HOH B 22 422 14 HOH HOH . H 4 HOH B 23 423 55 HOH HOH . H 4 HOH B 24 424 150 HOH HOH . H 4 HOH B 25 425 74 HOH HOH . H 4 HOH B 26 426 146 HOH HOH . H 4 HOH B 27 427 119 HOH HOH . H 4 HOH B 28 428 121 HOH HOH . H 4 HOH B 29 429 65 HOH HOH . H 4 HOH B 30 430 131 HOH HOH . H 4 HOH B 31 431 62 HOH HOH . H 4 HOH B 32 432 30 HOH HOH . H 4 HOH B 33 433 13 HOH HOH . H 4 HOH B 34 434 24 HOH HOH . H 4 HOH B 35 435 81 HOH HOH . H 4 HOH B 36 436 86 HOH HOH . H 4 HOH B 37 437 153 HOH HOH . H 4 HOH B 38 438 60 HOH HOH . H 4 HOH B 39 439 147 HOH HOH . H 4 HOH B 40 440 43 HOH HOH . H 4 HOH B 41 441 154 HOH HOH . H 4 HOH B 42 442 29 HOH HOH . H 4 HOH B 43 443 26 HOH HOH . H 4 HOH B 44 444 129 HOH HOH . H 4 HOH B 45 445 54 HOH HOH . H 4 HOH B 46 446 92 HOH HOH . H 4 HOH B 47 447 95 HOH HOH . H 4 HOH B 48 448 113 HOH HOH . H 4 HOH B 49 449 144 HOH HOH . H 4 HOH B 50 450 32 HOH HOH . H 4 HOH B 51 451 61 HOH HOH . H 4 HOH B 52 452 156 HOH HOH . H 4 HOH B 53 453 76 HOH HOH . H 4 HOH B 54 454 68 HOH HOH . H 4 HOH B 55 455 80 HOH HOH . H 4 HOH B 56 456 152 HOH HOH . H 4 HOH B 57 457 155 HOH HOH . H 4 HOH B 58 458 35 HOH HOH . H 4 HOH B 59 459 151 HOH HOH . H 4 HOH B 60 460 118 HOH HOH . H 4 HOH B 61 461 107 HOH HOH . H 4 HOH B 62 462 149 HOH HOH . H 4 HOH B 63 463 139 HOH HOH . H 4 HOH B 64 464 105 HOH HOH . H 4 HOH B 65 465 161 HOH HOH . H 4 HOH B 66 466 126 HOH HOH . H 4 HOH B 67 467 114 HOH HOH . H 4 HOH B 68 468 110 HOH HOH . H 4 HOH B 69 469 140 HOH HOH . H 4 HOH B 70 470 148 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 2NV . . . F 2 19.621 -22.338 4.326 1 100.67 ? N1 2NV 301 B 1 HETATM 2 C C2 2NV . . . F 2 20.486 -21.155 4.514 1 107.59 ? C2 2NV 301 B 1 HETATM 3 C C3 2NV . . . F 2 20.981 -21.139 5.963 1 96.95 ? C3 2NV 301 B 1 HETATM 4 O O4 2NV . . . F 2 21.979 -20.136 6.178 1 86.63 ? O4 2NV 301 B 1 HETATM 5 C C5 2NV . . . F 2 21.447 -18.824 6.37 1 95.48 ? C5 2NV 301 B 1 HETATM 6 C C6 2NV . . . F 2 20.961 -18.628 7.805 1 93.81 ? C6 2NV 301 B 1 HETATM 7 O O7 2NV . . . F 2 19.632 -18.093 7.808 1 104.03 ? O7 2NV 301 B 1 HETATM 8 C C8 2NV . . . F 2 19.581 -16.682 7.577 1 111.5 ? C8 2NV 301 B 1 HETATM 9 C C9 2NV . . . F 2 18.413 -16.356 6.655 1 111.43 ? C9 2NV 301 B 1 HETATM 10 O O10 2NV . . . F 2 18.018 -14.994 6.821 1 135.1 ? O10 2NV 301 B 1 HETATM 11 C C11 2NV . . . F 2 18.719 -14.071 5.986 1 143.06 ? C11 2NV 301 B 1 HETATM 12 C C12 2NV . . . F 2 18.15 -12.67 6.208 1 140.78 ? C12 2NV 301 B 1 HETATM 13 O O13 2NV . . . F 2 19.205 -11.705 6.257 1 133.51 ? O13 2NV 301 B 1 HETATM 14 C C14 2NV . . . F 2 19.474 -11.081 5 1 126.38 ? C14 2NV 301 B 1 HETATM 15 C C15 2NV . . . F 2 20.971 -10.814 4.851 1 120.56 ? C15 2NV 301 B 1 HETATM 16 O O16 2NV . . . F 2 21.547 -10.379 6.087 1 110.72 ? O16 2NV 301 B 1 HETATM 17 C C17 2NV . . . F 2 21.095 -9.092 6.518 1 98.06 ? C17 2NV 301 B 1 HETATM 18 C C18 2NV . . . F 2 22.275 -8.25 6.95 1 89.37 ? C18 2NV 301 B 1 HETATM 19 C C2A 2NV . . . F 2 21.624 -21.181 3.492 1 101.63 ? C2A 2NV 301 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #