data_1XL6 # _model_server_result.job_id d7Y-LTFt4i1DDupNizBXow _model_server_result.datetime_utc '2024-12-23 07:07:03' _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 1xl6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":3001}' # _entry.id 1XL6 # _exptl.entry_id 1XL6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 202.34 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _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 90 _cell.angle_gamma 90 _cell.entry_id 1XL6 _cell.length_a 105.756 _cell.length_b 107.532 _cell.length_c 89.654 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XL6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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,G,H,I,J,K,L,M _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' 2_645 -x+1,-y-1,z -1 0 0 0 -1 0 0 0 1 105.756 -107.532 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id K _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 metalc ? metalc1 A O THR 96 A THR 96 1_555 F K K . A K 1003 1_555 ? ? ? ? D ? ? ? ? ? ? ? 2.886 ? metalc ? metalc2 A OG1 THR 96 A THR 96 1_555 F K K . A K 1003 1_555 ? ? ? ? D ? ? ? ? ? ? ? 2.898 ? metalc ? metalc3 A O THR 96 A THR 96 1_555 H K K . A K 1006 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.71 ? metalc ? metalc4 A O ILE 97 A ILE 97 1_555 J K K . B K 1005 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.645 ? metalc ? metalc5 A O GLY 98 A GLY 98 1_555 G K K . A K 1004 1_555 ? ? ? ? D ? ? ? ? ? ? ? 2.581 ? metalc ? metalc6 A O TYR 99 A TYR 99 1_555 E K K . A K 1002 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.549 ? metalc ? metalc7 E K K . A K 1002 1_555 B O TYR 99 B TYR 99 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc8 F K K . A K 1003 1_555 B O THR 96 B THR 96 1_555 ? D ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc9 G K K . A K 1004 1_555 L O HOH . A HOH 2002 1_555 ? D ? ? D ? ? ? ? ? ? ? 2.878 ? metalc ? metalc10 G K K . A K 1004 1_555 B O GLY 98 B GLY 98 1_555 ? D ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc11 H K K . A K 1006 1_555 B O THR 96 B THR 96 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc12 H K K . A K 1006 1_555 M O HOH . B HOH 3002 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.775 ? metalc ? metalc13 I MG MG . A MG 2001 1_555 L O HOH . A HOH 2003 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.979 ? metalc ? metalc14 B O ILE 97 B ILE 97 1_555 J K K . B K 1005 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.513 ? # _chem_comp.formula 'C10 H26 N4' _chem_comp.formula_weight 202.34 _chem_comp.id SPM _chem_comp.mon_nstd_flag . _chem_comp.name SPERMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 SPM sing 290 n n N1 HN11 SPM sing 291 n n N1 HN12 SPM sing 292 n n C2 C3 SPM sing 293 n n C2 H21 SPM sing 294 n n C2 H22 SPM sing 295 n n C3 C4 SPM sing 296 n n C3 H31 SPM sing 297 n n C3 H32 SPM sing 298 n n C4 N5 SPM sing 299 n n C4 H41 SPM sing 300 n n C4 H42 SPM sing 301 n n N5 C6 SPM sing 302 n n N5 HN5 SPM sing 303 n n C6 C7 SPM sing 304 n n C6 H61 SPM sing 305 n n C6 H62 SPM sing 306 n n C7 C8 SPM sing 307 n n C7 H71 SPM sing 308 n n C7 H72 SPM sing 309 n n C8 C9 SPM sing 310 n n C8 H81 SPM sing 311 n n C8 H82 SPM sing 312 n n C9 N10 SPM sing 313 n n C9 H91 SPM sing 314 n n C9 H92 SPM sing 315 n n N10 C11 SPM sing 316 n n N10 HN0 SPM sing 317 n n C11 C12 SPM sing 318 n n C11 H111 SPM sing 319 n n C11 H112 SPM sing 320 n n C12 C13 SPM sing 321 n n C12 H121 SPM sing 322 n n C12 H122 SPM sing 323 n n C13 N14 SPM sing 324 n n C13 H131 SPM sing 325 n n C13 H132 SPM sing 326 n n N14 HN41 SPM sing 327 n n N14 HN42 SPM sing 328 n n # _atom_sites.entry_id 1XL6 _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 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0093 _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] 0.011154 _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 K A 1 1000 1000 K K . D 2 K A 1 1001 1001 K K . E 2 K A 1 1002 1002 K K . F 2 K A 1 1003 1003 K K . G 2 K A 1 1004 1004 K K . H 2 K A 1 1006 1006 K K . I 3 MG A 1 2001 2001 MG MG . J 2 K B 1 1005 1005 K K . K 4 SPM B 1 3001 3001 SPM SPM . L 5 HOH A 1 2002 1007 HOH HOH . L 5 HOH A 2 2003 2002 HOH HOH . L 5 HOH A 3 2004 4 HOH HOH . L 5 HOH A 4 2005 5 HOH HOH . L 5 HOH A 5 2006 7 HOH HOH . L 5 HOH A 6 2007 8 HOH HOH . L 5 HOH A 7 2008 9 HOH HOH . L 5 HOH A 8 2009 10 HOH HOH . L 5 HOH A 9 2010 11 HOH HOH . L 5 HOH A 10 2011 13 HOH HOH . L 5 HOH A 11 2012 14 HOH HOH . L 5 HOH A 12 2013 15 HOH HOH . L 5 HOH A 13 2014 17 HOH HOH . L 5 HOH A 14 2015 35 HOH HOH . L 5 HOH A 15 2016 36 HOH HOH . L 5 HOH A 16 2017 37 HOH HOH . L 5 HOH A 17 2018 44 HOH HOH . L 5 HOH A 18 2019 46 HOH HOH . L 5 HOH A 19 2020 47 HOH HOH . L 5 HOH A 20 2021 49 HOH HOH . M 5 HOH B 1 3002 1008 HOH HOH . M 5 HOH B 2 3003 1 HOH HOH . M 5 HOH B 3 3004 2 HOH HOH . M 5 HOH B 4 3005 3 HOH HOH . M 5 HOH B 5 3006 6 HOH HOH . M 5 HOH B 6 3007 12 HOH HOH . M 5 HOH B 7 3008 16 HOH HOH . M 5 HOH B 8 3009 18 HOH HOH . M 5 HOH B 9 3010 19 HOH HOH . M 5 HOH B 10 3011 20 HOH HOH . M 5 HOH B 11 3012 21 HOH HOH . M 5 HOH B 12 3013 22 HOH HOH . M 5 HOH B 13 3014 23 HOH HOH . M 5 HOH B 14 3015 24 HOH HOH . M 5 HOH B 15 3016 25 HOH HOH . M 5 HOH B 16 3017 26 HOH HOH . M 5 HOH B 17 3018 27 HOH HOH . M 5 HOH B 18 3019 28 HOH HOH . M 5 HOH B 19 3020 29 HOH HOH . M 5 HOH B 20 3021 30 HOH HOH . M 5 HOH B 21 3022 31 HOH HOH . M 5 HOH B 22 3023 32 HOH HOH . M 5 HOH B 23 3024 33 HOH HOH . M 5 HOH B 24 3025 34 HOH HOH . M 5 HOH B 25 3026 38 HOH HOH . M 5 HOH B 26 3027 39 HOH HOH . M 5 HOH B 27 3028 40 HOH HOH . M 5 HOH B 28 3029 41 HOH HOH . M 5 HOH B 29 3030 42 HOH HOH . M 5 HOH B 30 3031 43 HOH HOH . M 5 HOH B 31 3032 45 HOH HOH . M 5 HOH B 32 3033 48 HOH HOH . M 5 HOH B 33 3034 50 HOH HOH . M 5 HOH B 34 3035 51 HOH HOH . M 5 HOH B 35 3036 52 HOH HOH . M 5 HOH B 36 3037 53 HOH HOH . M 5 HOH B 37 3038 54 HOH HOH . M 5 HOH B 38 3039 55 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 SPM . E . K 4 51.885 -55.492 199.469 0.13 61.22 ? N1 SPM 3001 B 1 HETATM 2 N N1 SPM . F . K 4 51.091 -52.309 199.417 0.13 60.16 ? N1 SPM 3001 B 1 HETATM 3 N N1 SPM . G . K 4 53.298 -55.379 205.037 0.25 59.16 ? N1 SPM 3001 B 1 HETATM 4 N N1 SPM . H . K 4 54.753 -53.661 205.263 0.25 59.76 ? N1 SPM 3001 B 1 HETATM 5 C C2 SPM . E . K 4 52.932 -54.463 199.376 0.13 61.28 ? C2 SPM 3001 B 1 HETATM 6 C C2 SPM . F . K 4 51.965 -53.49 199.446 0.13 60.48 ? C2 SPM 3001 B 1 HETATM 7 C C2 SPM . G . K 4 52.28 -55.092 204.052 0.25 59.8 ? C2 SPM 3001 B 1 HETATM 8 C C2 SPM . H . K 4 53.912 -53.971 204.13 0.25 60.71 ? C2 SPM 3001 B 1 HETATM 9 C C3 SPM . E . K 4 52.736 -53.528 198.146 0.13 61.34 ? C3 SPM 3001 B 1 HETATM 10 C C3 SPM . F . K 4 52.964 -53.511 198.25 0.13 60.69 ? C3 SPM 3001 B 1 HETATM 11 C C3 SPM . G . K 4 52.883 -54.469 202.791 0.25 60.65 ? C3 SPM 3001 B 1 HETATM 12 C C3 SPM . H . K 4 54.098 -52.986 202.951 0.25 60.65 ? C3 SPM 3001 B 1 HETATM 13 C C4 SPM . E . K 4 52.81 -54.324 196.813 0.13 61.04 ? C4 SPM 3001 B 1 HETATM 14 C C4 SPM . F . K 4 52.215 -53.566 196.892 0.13 60.57 ? C4 SPM 3001 B 1 HETATM 15 C C4 SPM . G . K 4 51.781 -54.051 201.817 0.25 60.48 ? C4 SPM 3001 B 1 HETATM 16 C C4 SPM . H . K 4 53.286 -53.495 201.754 0.25 60.86 ? C4 SPM 3001 B 1 HETATM 17 N N5 SPM . E . K 4 52.852 -53.442 195.625 0.13 60.98 ? N5 SPM 3001 B 1 HETATM 18 N N5 SPM . F . K 4 53.111 -53.394 195.724 0.13 60.57 ? N5 SPM 3001 B 1 HETATM 19 N N5 SPM . G . K 4 52.34 -53.37 200.69 0.13 60.44 ? N5 SPM 3001 B 1 HETATM 20 N N5 SPM . H . K 4 53.295 -52.637 200.576 0.13 60.74 ? N5 SPM 3001 B 1 HETATM 21 C C6 SPM . E . K 4 52.761 -54.229 194.358 0.13 60.93 ? C6 SPM 3001 B 1 HETATM 22 C C6 SPM . F . K 4 52.392 -53.699 194.45 0.13 60.67 ? C6 SPM 3001 B 1 HETATM 23 C C6 SPM . G . K 4 52.142 -54.161 199.474 0.13 61.01 ? C6 SPM 3001 B 1 HETATM 24 C C6 SPM . H . K 4 52.369 -53.141 199.575 0.13 60.97 ? C6 SPM 3001 B 1 HETATM 25 C C7 SPM . E . K 4 52.815 -53.336 193.08 0.13 60.7 ? C7 SPM 3001 B 1 HETATM 26 C C7 SPM . F . K 4 53.264 -53.468 193.176 0.13 60.57 ? C7 SPM 3001 B 1 HETATM 27 C C7 SPM . G . K 4 52.703 -53.428 198.237 0.13 61.34 ? C7 SPM 3001 B 1 HETATM 28 C C7 SPM . H . K 4 52.974 -53.042 198.151 0.13 61.29 ? C7 SPM 3001 B 1 HETATM 29 C C8 SPM . E . K 4 52.754 -54.193 191.783 0.13 60.36 ? C8 SPM 3001 B 1 HETATM 30 C C8 SPM . F . K 4 52.4 -53.53 191.882 0.13 60.42 ? C8 SPM 3001 B 1 HETATM 31 C C8 SPM . G . K 4 52.548 -54.293 196.982 0.13 61.4 ? C8 SPM 3001 B 1 HETATM 32 C C8 SPM . H . K 4 52.13 -53.694 197.033 0.13 61.32 ? C8 SPM 3001 B 1 HETATM 33 C C9 SPM . E . K 4 52.806 -53.316 190.503 0.13 60.04 ? C9 SPM 3001 B 1 HETATM 34 C C9 SPM . F . K 4 53.247 -53.289 190.604 0.13 60.15 ? C9 SPM 3001 B 1 HETATM 35 C C9 SPM . G . K 4 53.093 -53.599 195.733 0.13 61.71 ? C9 SPM 3001 B 1 HETATM 36 C C9 SPM . H . K 4 52.882 -53.537 195.682 0.13 61.55 ? C9 SPM 3001 B 1 HETATM 37 N N10 SPM . E . K 4 52.747 -54.144 189.266 0.13 60.15 ? N10 SPM 3001 B 1 HETATM 38 N N10 SPM . F . K 4 52.416 -53.34 189.372 0.13 60.33 ? N10 SPM 3001 B 1 HETATM 39 N N10 SPM . G . K 4 52.915 -54.437 194.549 0.13 62.15 ? N10 SPM 3001 B 1 HETATM 40 N N10 SPM . H . K 4 52.162 -54.073 194.486 0.13 61.87 ? N10 SPM 3001 B 1 HETATM 41 C C11 SPM . E . K 4 52.538 -53.303 188.038 0.25 59.44 ? C11 SPM 3001 B 1 HETATM 42 C C11 SPM . F . K 4 53.272 -53.396 188.139 0.25 59.86 ? C11 SPM 3001 B 1 HETATM 43 C C11 SPM . G . K 4 52.857 -53.624 193.342 0.13 62.31 ? C11 SPM 3001 B 1 HETATM 44 C C11 SPM . H . K 4 52.924 -53.724 193.235 0.13 61.96 ? C11 SPM 3001 B 1 HETATM 45 C C12 SPM . E . K 4 52.833 -54.078 186.738 0.25 58.43 ? C12 SPM 3001 B 1 HETATM 46 C C12 SPM . F . K 4 52.443 -53.439 186.837 0.25 59 ? C12 SPM 3001 B 1 HETATM 47 C C12 SPM . G . K 4 52.757 -54.485 192.078 0.13 62.43 ? C12 SPM 3001 B 1 HETATM 48 C C12 SPM . H . K 4 52.047 -53.669 191.963 0.13 62.08 ? C12 SPM 3001 B 1 HETATM 49 C C13 SPM . E . K 4 52.589 -53.177 185.496 0.25 58.73 ? C13 SPM 3001 B 1 HETATM 50 C C13 SPM . F . K 4 53.381 -53.49 185.604 0.25 59.49 ? C13 SPM 3001 B 1 HETATM 51 C C13 SPM . G . K 4 52.684 -53.597 190.832 0.13 62.35 ? C13 SPM 3001 B 1 HETATM 52 C C13 SPM . H . K 4 52.884 -53.247 190.734 0.13 61.82 ? C13 SPM 3001 B 1 HETATM 53 N N14 SPM . E . K 4 52.849 -53.89 184.212 0.25 56.99 ? N14 SPM 3001 B 1 HETATM 54 N N14 SPM . F . K 4 52.636 -53.521 184.312 0.25 57.94 ? N14 SPM 3001 B 1 HETATM 55 N N14 SPM . G . K 4 52.558 -54.413 189.656 0.13 62.81 ? N14 SPM 3001 B 1 HETATM 56 N N14 SPM . H . K 4 52.056 -53.146 189.544 0.13 62.23 ? N14 SPM 3001 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 56 #