data_6BMN # _model_server_result.job_id M7mH3BjJE0t7Z0Id3gWn3A _model_server_result.datetime_utc '2024-11-22 00:35:12' _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 6bmn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":403}' # _entry.id 6BMN # _exptl.entry_id 6BMN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 6BMN _cell.length_a 99.541 _cell.length_b 99.541 _cell.length_c 158.386 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BMN _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id I _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 covale ? covale1 B C HIS 151 B HIS 155 1_555 B N CME 152 B CME 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 B C CME 152 B CME 156 1_555 B N PRO 153 B PRO 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? metalc ? metalc1 A SG CYS 124 A CYS 128 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc2 A SG CYS 127 A CYS 131 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc3 A ND1 HIS 137 A HIS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc4 A SG CYS 138 A CYS 142 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc5 A SG CYS 141 A CYS 145 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc6 A SG CYS 144 A CYS 148 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc7 A ND1 HIS 151 A HIS 155 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc8 A SG CYS 158 A CYS 162 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc9 B SG CYS 124 B CYS 128 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc10 B SG CYS 127 B CYS 131 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc11 B ND1 HIS 137 B HIS 141 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc12 B SG CYS 138 B CYS 142 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc13 B SG CYS 141 B CYS 145 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc14 B SG CYS 144 B CYS 148 1_555 G ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc15 B ND1 HIS 151 B HIS 155 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc16 B SG CYS 158 B CYS 162 1_555 H ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id PAP _chem_comp.mon_nstd_flag . _chem_comp.name "3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B PAP doub 258 n n PB O2B PAP sing 259 n n PB O3B PAP sing 260 n n PB O3A PAP sing 261 n n O2B HOB2 PAP sing 262 n n O3B HOB3 PAP sing 263 n n PA O1A PAP doub 264 n n PA O2A PAP sing 265 n n PA O3A PAP sing 266 n n PA O5' PAP sing 267 n n O2A HOA2 PAP sing 268 n n O5' C5' PAP sing 269 n n C5' C4' PAP sing 270 n n C5' "H5'1" PAP sing 271 n n C5' "H5'2" PAP sing 272 n n C4' O4' PAP sing 273 n n C4' C3' PAP sing 274 n n C4' H4' PAP sing 275 n n O4' C1' PAP sing 276 n n C3' O3' PAP sing 277 n n C3' C2' PAP sing 278 n n C3' H3' PAP sing 279 n n O3' P PAP sing 280 n n P O1 PAP doub 281 n n P O2 PAP sing 282 n n P O3 PAP sing 283 n n O2 HO2 PAP sing 284 n n O3 HO3 PAP sing 285 n n C2' O2' PAP sing 286 n n C2' C1' PAP sing 287 n n C2' H2' PAP sing 288 n n O2' HO2' PAP sing 289 n n C1' N9 PAP sing 290 n n C1' H1' PAP sing 291 n n N9 C8 PAP sing 292 n y N9 C4 PAP sing 293 n y C8 N7 PAP doub 294 n y C8 H8 PAP sing 295 n n N7 C5 PAP sing 296 n y C5 C6 PAP sing 297 n y C5 C4 PAP doub 298 n y C6 N6 PAP sing 299 n n C6 N1 PAP doub 300 n y N6 HN61 PAP sing 301 n n N6 HN62 PAP sing 302 n n N1 C2 PAP sing 303 n y C2 N3 PAP doub 304 n y C2 H2 PAP sing 305 n n N3 C4 PAP sing 306 n y # _atom_sites.entry_id 6BMN _atom_sites.fract_transf_matrix[1][1] 0.010046 _atom_sites.fract_transf_matrix[1][2] 0.0058 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0116 _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] 0.006314 _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 3 ZN A 1 401 401 ZN ZN . D 3 ZN A 1 402 402 ZN ZN . E 4 PO4 A 1 403 601 PO4 PO4 . F 4 PO4 A 1 404 602 PO4 PO4 . G 3 ZN B 1 401 401 ZN ZN . H 3 ZN B 1 402 402 ZN ZN . I 5 PAP B 1 403 501 PAP ACO . J 4 PO4 B 1 404 601 PO4 PO4 . K 6 HOH A 1 501 26 HOH HOH . K 6 HOH A 2 502 28 HOH HOH . L 6 HOH B 1 501 3 HOH HOH . L 6 HOH B 2 502 14 HOH HOH . L 6 HOH B 3 503 18 HOH HOH . L 6 HOH B 4 504 6 HOH HOH . L 6 HOH B 5 505 19 HOH HOH . L 6 HOH B 6 506 15 HOH HOH . L 6 HOH B 7 507 7 HOH HOH . L 6 HOH B 8 508 9 HOH HOH . L 6 HOH B 9 509 13 HOH HOH . L 6 HOH B 10 510 16 HOH HOH . L 6 HOH B 11 511 11 HOH HOH . L 6 HOH B 12 512 2 HOH HOH . L 6 HOH B 13 513 17 HOH HOH . L 6 HOH B 14 514 32 HOH HOH . L 6 HOH B 15 515 4 HOH HOH . L 6 HOH B 16 516 24 HOH HOH . L 6 HOH B 17 517 25 HOH HOH . L 6 HOH B 18 518 20 HOH HOH . L 6 HOH B 19 519 12 HOH HOH . L 6 HOH B 20 520 5 HOH HOH . L 6 HOH B 21 521 31 HOH HOH . L 6 HOH B 22 522 30 HOH HOH . L 6 HOH B 23 523 29 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 P PB PAP . . . I 5 -9.325 -11.907 0.626 1 74.69 ? PB PAP 403 B 1 HETATM 2 O O1B PAP . . . I 5 -10.55 -11.603 -0.454 1 72.43 ? O1B PAP 403 B 1 HETATM 3 O O2B PAP . . . I 5 -8.452 -13.015 0.125 1 81.02 ? O2B PAP 403 B 1 HETATM 4 O O3B PAP . . . I 5 -9.945 -12.337 1.92 1 100.73 -1 O3B PAP 403 B 1 HETATM 5 P PA PAP . . . I 5 -6.967 -10.186 0.199 1 115.91 ? PA PAP 403 B 1 HETATM 6 O O1A PAP . . . I 5 -6.715 -11.086 -1.02 1 94.71 -1 O1A PAP 403 B 1 HETATM 7 O O2A PAP . . . I 5 -6.937 -8.786 -0.241 1 98.67 ? O2A PAP 403 B 1 HETATM 8 O O3A PAP . . . I 5 -8.439 -10.528 0.859 1 94.06 ? O3A PAP 403 B 1 HETATM 9 O O5' PAP . . . I 5 -5.696 -10.44 1.32 1 105.48 ? O5' PAP 403 B 1 HETATM 10 C C5' PAP . . . I 5 -5.898 -10.446 2.738 1 99.85 ? C5' PAP 403 B 1 HETATM 11 C C4' PAP . . . I 5 -6.635 -9.204 3.245 1 112.73 ? C4' PAP 403 B 1 HETATM 12 O O4' PAP . . . I 5 -7.92 -9.445 3.403 1 106.78 ? O4' PAP 403 B 1 HETATM 13 C C3' PAP . . . I 5 -6.107 -8.84 4.705 1 123.56 ? C3' PAP 403 B 1 HETATM 14 O O3' PAP . . . I 5 -6.068 -7.537 4.881 1 131.47 ? O3' PAP 403 B 1 HETATM 15 P P PAP . . . I 5 -4.575 -6.744 4.599 1 165.66 ? P PAP 403 B 1 HETATM 16 O O1 PAP . . . I 5 -3.782 -7.534 3.565 1 129.4 ? O1 PAP 403 B 1 HETATM 17 O O2 PAP . . . I 5 -4.824 -5.35 4.08 1 155.94 -1 O2 PAP 403 B 1 HETATM 18 O O3 PAP . . . I 5 -3.765 -6.671 5.919 1 123.05 ? O3 PAP 403 B 1 HETATM 19 C C2' PAP . . . I 5 -7.114 -9.503 5.69 1 115.02 ? C2' PAP 403 B 1 HETATM 20 O O2' PAP . . . I 5 -7.555 -8.536 6.684 1 121.91 ? O2' PAP 403 B 1 HETATM 21 C C1' PAP . . . I 5 -8.162 -9.945 4.968 1 111.8 ? C1' PAP 403 B 1 HETATM 22 N N9 PAP . . . I 5 -8.239 -11.375 5 1 118.07 ? N9 PAP 403 B 1 HETATM 23 C C8 PAP . . . I 5 -8.221 -12.216 3.968 1 118.14 ? C8 PAP 403 B 1 HETATM 24 N N7 PAP . . . I 5 -8.304 -13.457 4.419 1 117.44 ? N7 PAP 403 B 1 HETATM 25 C C5 PAP . . . I 5 -8.382 -13.391 5.742 1 108.44 ? C5 PAP 403 B 1 HETATM 26 C C6 PAP . . . I 5 -8.489 -14.394 6.697 1 105.27 ? C6 PAP 403 B 1 HETATM 27 N N6 PAP . . . I 5 -8.53 -15.792 6.312 1 97.62 ? N6 PAP 403 B 1 HETATM 28 N N1 PAP . . . I 5 -8.554 -14.105 7.977 1 115.67 ? N1 PAP 403 B 1 HETATM 29 C C2 PAP . . . I 5 -8.514 -12.791 8.369 1 120.09 ? C2 PAP 403 B 1 HETATM 30 N N3 PAP . . . I 5 -8.411 -11.809 7.445 1 132.37 ? N3 PAP 403 B 1 HETATM 31 C C4 PAP . . . I 5 -8.343 -12.114 6.115 1 114.78 ? C4 PAP 403 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #